Just to close this out for those of you who might take an interest...
Klipsch was very helpful and passed me the appropriate service manual which basically is a short overview of the circuits, a bill of materials and the schematics.
The +/- 12V supplies are at the main amp board and they were functional after the lightening strike. The control board has series resistors in line with the supplies and I could tell that the control board was in trouble and loading the supplies. The board has 6 AN6551 opamps on it and it was easy to see just from the odd way the turn on circuit was behaving that at least one of those was disabled. I replaced all 6 thanks to Mouser with KA4558. The AN6551 are hard to find and a bit pricy with those who have a few trying to capitalize. The KA4558 are equivalents for like 60 cents.
With the new opamps the board was still not functional. I then proceeded with a blanket replacement of all the caps. I'll plug Digi-Key for that.
After replacing the capacitors the subwoofer would power off and on automatically in response to audio signal but still would not boom. I noted that flipping the phase switch generated a sutible deflection in the cone and that the main amplifier seemed anxious to move some air. So why wasn't signal getting through? There was obviously signal through to the audio detect and power on stage. There was obviously signal from the phase inverted opamp through to the power amp. In between there is a high pass filter which is supposed to roll off below 20Hz followed by an odd transistor-based diode clamp followed by a tunable low pass filter. There was no signal after the high pass filter. In face the output of that stage was clamped.
So while the capacitors for that high pass stage were correct and I replaced them with the corect values the two related resistor did not match the schematics. Are these tuned by hand? Was there a production deviation? I don't know but R1 was 7.5K instead of 14K and R19 was 619K instead of 240K. The replacement opamps must have just enough different in input offset current to put that 619K out of the stable operating range. Replacing those resistance with the proper ones (or, um, what I had that was real close) got me back up and shaking the house.
It's just interesting. Did you non-electrical engineering types out there follow this? Fun. Other than my wife who appreciates that I didn't drop the $2,200 for the RT-12d or the insurance company who gets away with covering a couple of lowly parts invoices, no one cares. But I have the low end back and I care!
Thanks for the help Klipsch with that manual.