Hi,
You seem to be an electronics "black belt"so I couldn´t hope to give you any meaningful advice at the very low level stuff, however, I am wondering whether you have tried the more down to earth advice usually dispensed on such occasions:
1) remove all socketed chips (does the A4000 have any?), daughterboard, processor cards, expansions and any peripherals, clean all connectors with isopropyl alcohol, look for wear&tear and reseat them. Check memory (simply remove simms bar one at a time).
2) check traces around the battery, acid leakage damage could conceivably progressively deteriorate over time. Clean area with appropriate chemical solution (some advise water, others vinegar, I would say check with someone who really knows first).
3) The either one IC work / both ICs won´t work deal makes me think it is related to power supply. Power supply damage also squares with the manner in which the problem occured to begin with (while the computer was on). You said you tried out voltages at the "power section" of the motherboard - not sure what you meant. Get an Atx to A4000 connector (amigamaniac in australia does them and so does amigakit I think) and try a new one.
4) Of course, another alternative is that one of the custom chips itself decided to give way. I don´t have a clue how you could check that though, sorry.
Good luck and keep us posted on progress - let us have more info on whatever else you´ve tried, it might stimulate further ideas.
