They're the same size, coincidentally. The size matches the scale, about, but VF-1s are much smaller than VF-25s.
Anyway, I'd suggest you just buy a good Gundam Marker - they're like $2.50 US - and panel line with that. The results will be much cleaner and look better.
That panel line you have right now looks like crap, to be honest. Get some alcohol and wash that out.
As for cutting decals for transformation, I can't help you with that unless I get my hands on it. My advice is to stick it down in Fighter, and use an X-Acto knife to cut it where there are places the fuselage splits. On that note, before transforming it, give it a nice coat of clear coat to seal it against wearing the decals.
Don't weather the nosecone just yet. Wait until the thing is done. If it looks too bright then, and doesn't complement the rest of the valkyrie, wash it with some grey or something.