Tools / supplies / parts needed:

A Jetfire or Valkyrie toy
White spray primer
Flat black spray paint
Gloss clear coat paint
Tamiya Acrylic paints
   Black
   White
   Desert Yellow
   Orange
   Green
Paint stripper
Airbrush
X-Acto knife with new blades
2 inch wide Masking tape
Small Phillips screwdriver
Sandpaper (320, 400, and 600 grit)

To begin with, keep in mind that this is only a guide. You don't exactly have to follow it to the letter. In fact, I'm sure the conversion would go faster if you covered several steps at once, so you could prep and paint a bunch of parts in one fell swoop. But none the less, I'm going to write this guide in a step-by-step manner, in an attempt to minimize confusion. If you do choose to do it your own way, just be sure to read far enough ahead so you know what to expect.
And when you're taking stuff apart, just make sure you don't lose ANY of the screws and smaller parts. I recommend storing them in a ziplock bag and keeping it somewhere safe.
Also, there are often a lot of imperfections in the plastic. Especially if you're converting a bootleg valk ;) I really recommend you take the time and sand down the uneven seams and the rough parts where the sprues were. The little things most definitely make a difference.

One final note. When you're done, don't expect this to be a toy you can play with like you could your old Jetfire. The whole thing's going to be painted, and paint is far from indestructible. It can chip off if you're not careful.

That having been said, let's get started.

We'll start with the legs first. Remove the 3 screws holding the bottom portion of each leg together, and pull the two halves apart. Store the spring, landing gear lever, and the washer by the feet in your ziplock bag.

Next, we're going to prep the pieces for painting. Start by removing any stickers that might be on them. Get rid of the sticky residue with some paint thinner on a rag or a Q-tip.
The inner leg pieces are made of metal and are pre-painted. I recommend stripping this paint off before proceeding to give the primer a better surface to stick to. Or at least rough the paint up a bit with your sandpaper.
To strip off the paint, soak the pieces in paint stripper or paint thinner for a while. Pine-Sol will also work in a pinch, but it'll probably take about 24 hours to get all the paint off. Once it's soaked for a while, brush it off with an old toothbrush and wash the part with water.
If you need to strip any plastic pieces, it is very important to make sure the stripper you're using won't damage the plastic. To test it, put a little of the stripper somewhere on the part that isn't visible when the toy's assembled, like the inside of a leg piece. Wait a while, and see if the plastic in that spot has gotten soft. If it has, don't even think about using it. I've found that Pine-Sol will strip just about any type of paint (given enough time), and doesn't attack 99% of plastics.

While the paint's stripping off the legs, we'll paint the feet. Begin by taking the halves of the feet apart (giving you 8 pieces total). Wash these with some warm water, dish soap, and a toothbrush. I recommend you do this to every piece you paint to avoid dirt and dust from getting trapped under your paint.

We're going to paint the feet a bit differently from most of the other pieces. The friction from moving the feet while transforming the toy can cause the paint to wear. In my first attempt, this happened and my white primer started to show through. To prevent this, paint them with Krylon ultra-flat black spray paint. Give them several light coats, followed by a few coats of clear coat. Allow plenty of time to dry to insure a hard, protective finish.
With this method, even if the paint wears down to the plastic, it won't be very noticeable, because the plastic is black too :)

Next we'll move onto the legs. And here's where it starts to get a bit complicated.
Make sure all the paint is gone from the metal pieces, including the panel line crevices. Wash off the outer leg pieces. When they're all dry, start priming them. Use white spray primer on them in light coats until they're evenly and completely covered. The rule of thumb is to make sure you can't see any of the original color through the primer.

Now comes our first real challenge... mixing paints. To finish the legs, we will need both tan and orange.
I've been stuck on Tamiya Acrylic paints for the past couple of years now. I love em. But the colors they offer don't quite match the colors I needed for this project. So I bought the closest ones I could get and mixed them as best I could.
The best thing I could to was kinda eyeball it. But fortunately, I have the laserdisc boxed set, so I threw in disc one, and paused it on a good image of Hikaru's VF-1D. For the tan, I started with Tamiya's 'Desert Yellow' and added white slowly until it looked about right. Tamiya's orange was pretty close, but it needed to be a bit darker. So I added a bit of red and it looked dead on!
If you can find some other good quality paint with the right colors, by all means, use them. But if you wind up mixing paints, one word of warning... Mix a LOT! You're going to go through more of it than you think. And trying to mix the same color twice is a paint in the ass. I wound up doing it 4 times when I made mine -_-

With that out of the way, we can start airbrushing. I'm going to assume you know the basics of airbrushing already (including paint thinning, cleaning, etc). Load up a jar of your tan paint and paint all 4 leg pieces completely and evenly. As always, use several thin coats, not one thick one. I recommend you paint the inside of the legs also, since you can see inside them when the landing gears are down. Also, paint the two small plastic pieces that were by the landing gears on both sides.

Next we have to paint the raised section on the legs orange. To do this, we'll mask off the outside with masking tape. I recommend applying a coat of clear coat to the pieces to help prevent the tape from pulling up the tan paint when it is removed.
Apply pieces of masking tape, overlapping the edge where the raised portion starts. Push it down a bit with your fingernail or a toothpick, so you can see the exact point where the raised section begins. Now take your X-Acto knife (with a NEW blade) and lightly cut the masking tape along that line. Be careful to only cut the tape, not the plastic below it. Remove the tape on the raised portion, and you're ready to paint.
Make sure everything except the raised section is masked off to avoid getting orange on them too. Now use your airbrush to paint the unmasked portion orange. When dry, remove the tape and seal the entire pieces with clear coat.

Step 1: Outer leg piece primed in white	Step 2: Entire piece painted tan and clear coat applied
Step 3: Piece of tape across area to be painted orange	Step 4: Tape pushed in along groove (highlighted in ink)
Step 5: Tape cut along the groove and removed	Step 6: Remainder of the piece completely masked off
Step 7: Painting the area orange	Step 8: Masking tape removed

Next, we'll work both parts of the upper legs. Not too tough.

Swing down a leg halfway as if you were going to transform it. On the back side of the metal piece, there are two screws. Remove them both. Now that the 'hip' is apart, we can take apart the 'thigh' (at least that's what I think you'd call it :P). Take out the last screw holding it together. Both sections have some small parts. As always, make sure you don't lose them.
The black parts on the 'thighs' are separate pieces of plastic. I've seen them attached two different ways.

Method 1: The two pieces are attached with plastic pegs that go through the main piece, then are melted on the opposite side to widen them, thus holding the two pieces together. To get them apart, take your X-Acto and cut off the melted plastic, until it's flush with the surface of the plastic on the inside of the thigh. You should then be able to push the black part out by pushing on the peg. Don't try to get them out any other way, or you could end up breaking the plastic. They're kinda thin in the middle.

Method 2: The two pieces are glued together. You can usually still get them apart though. Just lift the black part up on each side. If there's any glue in there, it should break free without too much trouble. Then take a screwdriver or something and push the black piece out through one of the holes in the white part.

Use these methods to completely disassemble what remains of both legs.

Painting these parts is pretty straightforward. For the black parts, including the big black shutters on the hips (but not the black, plastic pins with the springs on them), paint them the same way you painted the feet. Flat spray paint and gloss clear coat. For the rest of the leg pieces, prime them white, then airbrush them tan. It goes without saying that you should clean the pieces the same way as you did the lower leg pieces. Remove the stickers, wash them, etc, etc. I probably won't bother to mention it again. Same thing with priming before airbrushing, and clear-coating afterwards. Just do it to everything :)

That out of the way, explaining how to do the arms will be a breeze.
Take out the two screws holding the shoulder pieces together. Then the two screws in the forearms. Then one last screw in the upper arm. Got all that? Good. Now paint them all tan :)

Next we're going to take apart the first part of the main body, the chest and nose. On the underside nose/chest, there's four screws, plus one holding the chest plate on a black, sliding piece of plastic, and another underneath the landing gear holding a spring in place. Remove them all.
With that done, you should be able to separate the two halves. You can also remove the head, cockpit, and the seat. Store away the landing gear and springs. If you ordered the full conversion kit from Chris, you'll have the new 2-pilot cockpit, and won't need the old one. For the head, you'll need to save the base that it mounts on, but the actual head is now useless. Do with it what you please. If you really want to, you can give it to me to show your eternal gratitude for writing this guide ^_^

First, we'll paint the two large pieces that form the nose. Like the legs, paint the inside also, at least in the front, under the landing gear. When that's done, and after the clear coat is completely dry, paint the black stripe across the nose. To do this, we'll use the same technique we used to paint the orange on the legs. Wrap a single piece of masking tape around that part of the nose, and use your fingernail, a toothpick, whatever, to push the tape down into the groove. Then use your X-Acto knife to cut along the grooves. Remove the tape in the center, and airbrush in your stripe with black paint.
black. Use the same technique I just explained for the nose stripe for these.

There also has to be a black stripe in the top center of the chest plate. To make this one, take 2 strips of masking tape and place them on the flat part of the plate, along the line where it curves up in the center. Place a third strip just below the top of the plate, along the top line of the engraved part in the middle (it would be the air brake if it actually worked). Tape up the rest of the piece to avoid getting paint where you don't want it. Also, be sure to tape up the edge on top of the chest plate, just above the part you're about to paint. Once that's done, airbrush the stripe in with black paint.

Next, we'll paint the plastic plugs on the metal hip joints. What remains of the hip pieces is connected with a metal rod. Push the hips together until one of the plugs come out. Then do the same with the other side. Paint, then replace them.

Next, paint the head mount bracket thingy tan.

And finally, our last major step, the back. It's held together by three screws, including 2 that are behind the metal parts that connect the arm mounts to the back. When that's apart, a bunch of stuff will be loose. Take the wings and that flip-up piece on the back and set them aside. If they haven't already fallen out, remove the metal pieces with the arm mounts attached to them. That same piece of the back will have 2 small black pieces in it. Those are what make the wings click when you move them. We don't need to remove those. They can get painted with the rest of the part. On the other half of the back, there's a spring-loaded piece that holds the arms in place in fighter mode. Leave that in place also.

We'll start simple. Take the arm mounts and remove the screw. Paint both plastic pieces tan. Leave them apart for the time being, we'll be dealing with the metal pieces in a bit.

Next we'll do the wings. First, paint them completely tan. After that's done and the clear coat is applied, we'll work on painting the orange stripe on the forward edge of the wing. Use the same masking tape trick as before. Be sure to cut along the 2 sets of grooves near the base of the wing (the searchlights) and leave tape on them when you paint the stripe. Also, be sure not to paint all the way to the tip of the wing. There's a vertical panel line about 1mm from the wing tip. Stop the stripe here.

Next is the flip-up thingy. I don't know what to call it, since it doesn't exist anywhere other than on the 1/55 toy. It's just there so the head has enough clearance to flip up. Anyway, paint the whole thing tan. Then we have to paint the rounded portion orange. In fighter mode, that orange part should look like it's a continuation of the chest plate (which, of course, is orange also), so we've gotta make it look good.
Use the normal masking tape technique to mask off everything else. On the flat side (which is on top in battroid mode), take a piece of tape and connect the two points where the curve starts. We want that area of the flat part to be orange also, otherwise the tan paint will show through the crack in fighter mode and the effect will be ruined. Getting back to the point... paint that area orange.

The backpack thingy can be kind of tricky to get apart. First, remove the two screws on the top. Then grab the top piece by the black thruster packs, and the bottom by the big plastic pieces in the front and back of the pack. Gently, try to pull them apart. They're sometimes glued together at the 1/2" long piece the tail fins swivel on. If they don't come apart easily, there's not a whole lot of advice I can give you... just be careful.

Once all that's apart, paint the 2 black thruster blocks black the same way we did the feet. Paint everything else tan, except the top of the backpack thing (the part with the screw holes). Both back pieces, the bottom of the backpack, and both tail fins need to be tan. On the bottom piece, there's a piece of plastic about half an inch long that goes over the post in the back of the piece. It's best if it gets painted separately.

Once that's done, we need to paint most of the tail fins orange. Just the strip on the back of the fin remains tan. Use the masking tape trick for this one yet again. While you're at it, paint the top the backpack orange.

With that out of the way, just about all the painting is done! Pretty much just the head should be left. But there's one extra step I took, painting the metal pieces. Only problem is that the paint can chip off them fairly easily, so I really only recommend painting them if you don't plan on playing with the finished toys much. But even if you don't plan on painting them, I really recommend polishing all the metal pieces. They're pretty ugly if you don't.

To do this, just sand them a lot. Start with the 320 grit sandpaper and work your way up to the 600 grit. Emory boards (nail files) can also make the job easier.

I couldn't find any better (i.e., more durable) method of painting them than the same priming and airbrushing techniques we've used so far. If you can think of something better, by all means, use it.

Finally, the last step of the painting process, the head. Follow Chris's guide to prepping the resin parts, then prime and paint them all tan. Next, we'll be painting the lasers and the eyes gray. Like when you mixed your tan paint, do a little research and try to match up the gray as best you can, mixing black and white paints.

Paint the head lasers gray from the area where it starts to taper inward, near the base, all the way to the top of the laser. For the actual head, get out a fairly small paintbrush, and paint the area 'around' the eyes. Not the actually surface of the eye, just the rectangular area around it. And try not to get any paint behind it either. Once that's done, clean off the brush, and paint the face of the eyes green.

There's a small trapezoid engraved on the top of the head. This need to be painted black. Either brush it in, or use our masking techniques. Up to you.

Now we begin the ever-fun reassembly process! By now, you've probably long forgotten how everything goes back together, so I'll walk you through it.