Hi Mike
I think that trying to reuse the electronics in a very old and outdated console is fraught with unseen problems and continuing repair adventures. By replacing the old electronics, all the pistons will become instantly programmable with Hauptwerk.
Several years ago i bought an Allen MOS 1 three manual console. I gutted the entire Allen electronics, keeping only the wiring from the pistons and pedalboard. It actually was very easy, requiring only a screwdriver and wire cutters. I bought the MOS 1 midi kit from Artisan Instruments
http://www.artisanorgans.com/. There are also other companies that offer such kits. (Google is our friend) I than wired the keyboards, pistons, and pedalboard to the Artisan input boards, plugged it in, and out came midi! Actually, of course, it did take me about a month or three to do the wiring. I gave the old Allen guts to a local Allen repair man to give to churches in need of the no longer available parts. The keyboard wiring I replaced with a harness from Peterson
http://www.petersonemp.com/. All together, the midi boards and wiring stuff came to about $1,500.00, making the total 3 manual console, pedalboard, and lots of finger and toe pistons come to just under $2,000. (plus my time, of course)
Good luck with your project!
James