After tracing more signals (and not finding anything out of order), I think the problem is a dodgy connection at the CPU or maybe ROM SIMM.
The last time it didn't work, I gave the CPU and ROM a good push and it started working. I have a socketed CPU and I've never pulled it out, if the problem gets worse I might try that.
The next weird problem: for some reason this SE/30 has an 800k floppy drive (MFD-51W-03)! It also has a Miniscribe 8425SA that isn't spinning up, I need to put that in an external enclosure and see if I can get it to spin. The HD has a real old production date (1986) for an SE/30, almost like this machine had SE drives swapped into it.