Partial success. I'm not sure what changed.. but here's what I did. First, I followed from pin 8 of B2 to every point it went to. Everything checked out, all had the correct signal and were connected. I then started following SOFT 5 from pin 8 of A2, which I think handles the CLR lines. They were low. Since pins 9 and 10 of A2 are tied to ground, the output should be high. To check whether it was the chip or something else pulling the line low, I bent out pin 8. Soon as I did that, I got a double beep - and this!
So now I know a few things - the crystal is good, nothing wrong with Phase 0 or Phase 1 clocks other than something was stopping them from operating. I bent pin 8 back in on A2.. the machine went back to zilch. I then removed A2 and plugged in another 74LS00.. machine still works.
I then went to try and investigate why it's crashing on boot. I read a bit on this and tried swapping the 8T97s with the originals - immediately on the first chip we were back to zilch again and it would *not* come back with replacement of the chip that was there. I then fooled around and reseated the CPU, really pressed it into socket (the socket plastic basically has separated at one end from the pins).. and got it back again.
So I think, unfortunately, I'm dealing with potentially multiple issues including socket and/or board issues. The board to my eye doesn't look rusty or anything.. very clean on the both sides.
Anyway, I will keep at it. At least I got something now!