Allen,
You may be better off to jettison the factory MIDI and install a new interface if you want to use the existing tabs, expression, crescendo, capture pistons, etc. Allen MIDI in 1987 was not designed with those features in mind.
On the other hand, if you could be content with augmenting the Allen voices with an external system such as HW or j-Organ, you might use a touch-screen monitor to control the stops, then have a competent organ audio person design an expression control that would tie into the Allen LDR expression shoes. Allen will sell you extra LDR cells for the existing shoes, if needed.
It's even possible, though costly, to tap into the Allen capture system and have the pistons simultaneously control the Allen moving stops and some external PC organ at the same time. This would involve some opto-isolators and other exotic components, but would work if you wanted it to.
But if you are planning to gut the console anyway, I'd just sell off the Allen components on ebay and use the cash to equip the console with a MIDI setup designed from the ground up to work with HW or Artisan.
John
Rodgers 890 at church.
Baldwin D422 at home.
Scads of old organs in the shop! H E L P !!!