The exotrain upgrade could simply allow your player, unmodified, to attach to the rail using the G key ("Connect train" default key in vanilla) as if your exoskeleton had wheels it could line up and start using. You would simply walk onto the track, and it would connect to the closest one to your feet.

Just as these vehicles still look like trucks, you could still look like a player--and not have to manage a completely separate item for rail attachment: https://en.wikipedia.org/wiki/Road-rail_vehicle

Creating an entire custom rail vehicle was a nice touch, but it seems to be causing some issues with reliably switching modes, and doesn't have to be so complicated. Can you use a 'train' with the player's power armor form as the model?