v1.0 ship was working fine until suddenly, I couldn't exit, couldn't enter, couldn't do anything with it. I have no idea if this was just Starfield being Starfield or if I messed something up in the CK when building the ship, but I resaved in CK and went back in-game. Probably Starfield being Starfield because it is odd that everything worked fine for a time before breaking.
Made slight changes to ship template by changing any references to Class A to Class C.
Completely remove the landing bay and then add it back if you have issues entering the ship after upgrading.