I opened up the thruster and checked out the problem. The ratchet for the feet articulation does have a front and back and has a screw that faces away from the landing gear. I try to remove the feet from the ratchet assembly but only the front was willing and the back did break. I glued it back together and reversed the feet do that it faces properly. But I had to modify the ratchet in order for it to fit backwards and clear the screw for the thruster pieces themselves. Sadly it does not work perfectly. It does go completely into the thruster in Fighter mode, but it does still transform and stand upright in Gerwalk and Battroid modes. It definitely would benefit from a replacement part, and I now consider myself an expert on the thruster/leg assembly. haha
Thanks Valkyrie addict for the reply and advice.