Oh, I should have mentioned that I'm not doing anything irreversable to the Vectrex. It'll even still play Vectrex games through MESS. That's part of why I'm having a hard time... I don't want to destroy the original guts to make this work.

The mobo has a PCI slot, but there's definitely no room to add an expansion card. It's a really, really tight fit.
Wow! Those joymice are really expensive! Thanks for pointing them out, though.
The original Vectrex controllers are analog. It's going to require some unique thinking to achieve my goal of making them work without modifying one because of the way they work. They take -5v and +5v input and vary the output between -3.25v and +3.25v. -3.25v is far left, 0v is center and +3.25v is far right. However, I'm not worried too much about coming up with a circuit to translate that into +0 through 5v.