So, I’m still trying to carefully go through things to make sure I know what does and doesn’t work, but the fact the mouse and keyboard just started working again is great, but troubling.
I don't think the intermittent keyboard/mouse issue is anything you're doing wrong. The one thing common that fits both symptoms is the input lock circuit. The front panel key switch disables data from the keyboard and the mouse movement - but not the mouse buttons.
The circuit is configured so that without the key switch connected, it'll default to the enabled state. If there's an issue with a poor solder joint, or cracked SMD resistor for example; that could create a floating input situation, which would explain the intermittent behaviour you're seeing. I'd start by checking pullup resistors R206 and R207, and all the solder joints on U131.
Have a look at page 4 of the schematic and you'll see what I mean. Note that the 7406 inverter gate is open collector output.
http://amiga.serveftp.net/Schematics/A4000_schematics/A4000_Rb_schematic.pdfThe expansion bus issues sound like a different issue, perhaps related to the riser. You should be able to narrow that down by a process of substitution as you're doing.
