Joe,
Don't wait another day. Order the service manual from MusicElectronics, as mentioned above. It's quite impossible to follow the signals through the organ without the manual at hand, and it doesn't cost very much.
That's not a simple organ by any means, but a competent tech with Baldwin experience should be able to get it going at a reasonable expense. It has a lot of good sounds and some interesting trinkets too, if you're into that.
You have some sort of simple audio problem, I think. There isn't any fancy keying circuitry in that organ, everything comes from the same tone generators and all stops are direct keyed right at the keyboards. So if some stops work, the others are just not getting through their particular stop-switching, tone filter, pre-amp, and audio amp circuits.
You could have a dead amplifier channel, and that would be easy to check. Just listen to each of the three speakers and see if anything at all comes from each one. The flutes will obviously be in the rotary speaker, bass in the 15" speaker, and the reeds and strings should be coming from the other (stationary) speaker. The rhythm and percussions should also come from the same speaker as the reeds and strings, but may be playing through the bass channel, and the reed/string amp may indeed be dead.
A dead amp in this model is often due to the output capacitor -- there is one on each channel -- having failed. This is an inexpensive part and easily replaced by a tech. You should also verify that the volume pot for that channel is not just resting on a dead spot -- turn it through it's range a few times.
Good luck.
John
Rodgers 890 at church.
Baldwin D422 at home.
Scads of old organs in the shop! H E L P !!!