Not running quite stable yet. It had run through a bunch of GEMBench loops before I went to bed, but crashed before the morning, and then would not boot again. Sticking a 68HC000 directly into the motherboard socket worked fine. I did not find any shorts or opens on the bus connections on my switcher board, but then by the time I removed the tower from the (soldered in) Lightning ST, I had a short between D1 and D2.
This is quite curious, because I found the exact same short yesterday, and thought it had been resolved by cleaning off a bit of mess from the Lightning. Not seeing any further mess, I cleaned up the Lightning with IPA again anyway, and the short disappeared again. What's really strange here, besides the same short showing up twice, is that I really don't think it was there before I removed the tower. But maybe I just missed it.
Since these passthrough pins have gotten a lot more in/out cycles than I wanted, I very gently bent out the pins on the Cloudy and Storm and reassembled, crossing my fingers it's the last time. As this is supposed to be a pretty permanent setup, inside a computer that isn't easy to open, I'm not opposed to flowing a little bit of solder from the side onto all of these pins, but since that significantly reduces my troubleshooting options, I don't want to do that unless I know it'll fix things up once and for all, which I can't know without doing it. Bit a chicken and egg problem there.
It's back to running GEMBench now, and I need to be doing actual work today, so it will have some alone time now, to either keep working or not.