XLR wiring is not really "all over the place", but rather one of two ways: 2 hot or 3 hot... If it's not what you want it to be, swapping the wires on pins 2 and 3 of all the XLRs is all that's necessary. Pin 1 on XLRs is always ground, because by design that pin makes contact first when mating connectors.
If pins 2-3 are not matching the signal sense of your other gear, and you have a balanced I/O setup, it won't hurt anything if it's plugged in that way. It will just have the wrong signal polarity (sometimes referred to as phase) and your speakers will go in when they should be going out and the leading edge of a given waveform.
If your system includes cables or equipment that unbalances balanced lines by shorting one lead to ground and letting the other become "hot", then it's theoretically possible some of the gear won't be happy. But since that method is so widely used, it's unlikely designers didn't plan for that in their work.
On the transport, there may be some lifter defeat logic that is selected to keep the tape lifters from operating. It's been awhile, but I think it was a remote function for MTR-10s and 12s so that timecode track could be read. Hopefully there was audio muting too!
If you dive into head replacement/refurb, I believe some of the shops would accept entire head blocks, lap the heads, and re-align before returning them. That would save a lot of work, especially if you don't have alignment tapes, etc. at the ready. If the heads and fixed guides are mounted to the block above them, rather than to the chassis, they can probably pull that off.
Chip
