The models of the Mech jeb capsule and the new adapter from the ARM update are swapped.

I have no such thing here. You'll have to check your install because I don't see how this could happend.

I inserted the MechJeb 2 game data folder contents into the ksp game data folder. That is how I did it in the previous versions of ksp with all mods including MJ, but I got a new version of MJ for 0.23.5 and it gave me that issue. I'm on Windows 7 32 bit