I would toss the electronics and go with a PMDX-126 BOB and Gecko 201X drives. I've done a bunch of retrofits on old machines and it's always easier to just start with new electronics rather than trying to get old, outdated stuff working. If you need a new motor power supply, Keling has pretty good deals on unregulated supplies.
Why do you need 2 parallel ports? Mach supports 6 axes. If you have X, A (slaved to X), Y, Z, and your basic limits, home and estop, you shouldn't need a second PP. If you do have a lot of additional inputs, the PMDX-126 has inputs for a second PP. In that case you would need a second PP in the PC.