There is still quite a bit that I didn't get a chance to address for this organ. So, for whoever has this instrument in the future, here's some things to watch out for:
The amplifier I rebuilt could use some more work: currently it turns on with a loud 'thud' when power is applied. This comes from the output being enabled while the power supply is still stabilizing and from the output capacitor charging up to Vcc/2. The amplifiers have a 'mute' function, there just needs to be a circuit to delay unmuting the amps for a second or so after power is applied and to make that unmuting gradual. (It should just take one transistor, a capacitor, and a resistor or two.) Actually, what I really wish I had time to do was build new amplifiers entirely. With a dual-sided power supply this issue goes away entirely.
There's some weirdness going on with the Great Bourdon 8' stop's transistor switch. Originally the stop control was connected through a resistor network tacked onto the back of the circuit board and one of the transistors in the transistor switch was burned out. This stop is supposed to activate both when its own stop is pulled and when the Great celeste stop is pulled, but it doesn't sound like that is happening. I pulled off the extra resistors and replaced the bad transistor but I can't hear any difference. I'm not sure what's going on there. The only real impact of this is that to make the Great celeste sound right you have to remember to pull the Bourdon stop as well.
The air sound doesn't seem to work. This circuit is supposed to inject some sort of hissing that sounds like the rushing of air from organ pipes. I'm told that it can be a subtle effect, but as far as I can hear the circuit doesn't do anything at all. I examined the circuit and found that it had been miswired -- the on/off switch was wired to the collector of Q285 instead of its base. I fixed this but still couldn't hear anything. Something may be out of adjustment in the noise generator part of the circuit (I suspect that part is finnicky and the miswiring may have made it unhappy), but I'd have needed my oscilloscope to troubleshoot it. The impression I got was that many disliked the air sound on this line of organs anyway, so this may be no loss.
Notes that correspond to oscillator number 17 are softer than all the others. This is true across most stops, including Pedal, Great, and Swell stops, so I think there is something wrong with the oscillator itself. I didn't get a chance to investigate any further.
I should also mention that there were some reports of the organ misbehaving mysteriously in church on occasion -- refusing to turn on, one keyboard suddenly going silent, etc. I never actually witnessed any of this, except for a cipher on one occasion, nor did anything like that occur when I was working on the organ at home. My best guess is that there might have been a loose connection that was jiggled back into place when the organ was transported from the church. Unfortunately, having never actually seen the problems, I can only guess.