Thanks for the advice, everyone.
I don't like the direction this is going. New CIAs - no difference. Removed J200 - no difference.
I pulled the entire motherboard - found a few solder-side legs that had snapped and cleared them away. Added some electrical tape between the plastic insulation and the RF shielding. Still no difference. I'll pull the board again for a closer look, but, assuming that fails, what are my options? What exactly are these EMI things? (i.e., what's the part called that I should use as a replacement?)
EDIT: Solved, finally!
Slathered the RF shielding in loads of electrical tape to add some additional insulation. Phew! What a mess this was.
EDIT2: Just kidding, not solved, actually. New symptoms, though. Works correctly with no accelerator installed, works correctly with the accelerator installed and disabled in software (A2630 right mouse button boot menu), does *not* work with the accelerator installed and fully enabled in 030 mode. I didn't add extra insulation directly under the CPU slot, so will try that next, otherwise... any more ideas?