After a bit of research, it seems that part of the Lisa ID is stored in the shift register at U976. When the Lisa ID is queried. If the incorrect ID is returned, it can mean that AGA modes are not available in workbench.
So what has gone wrong here? The U976 is a 74HCT166 shift register (datasheet here: https://www.farnell.com/datasheets/2030248.pdf) which, along with sampling the bits from the 'mystery' J975 header, has two static input bits that make up the Lisa ID which should be at logic 0. Some details on this (and the mystery header) here: http://www.zimmers.net/cbmpics/cbm/amiga/a4000jumpers.html.
These are the two bits used in the Lisa ID shown tied to ground:
I confirmed these pins were indeed connected to ground on the motherboard.
So, on with the probes:
Another visit to my trusty electronics part retailer and I ordered replacements for both shift registers U976, U975. I also ordered a replacement for U177, which is a 5 bit flip-flop, that latches the output of the real time clock chip... datasheet here:https://www.farnell.com/datasheets/2030248.pdf. I figured I'd replace this as well, as although it appeared functional , I'm not sure I trusted it to last with the level of corrosion it had suffered.
Once the chips had arrived, I masked up the board ready to replace the chips.
So, did it work?....
Great! Lisa now has the right ID (fcf8, rather than fff8), and Amiga Test Kit is happy, thus I am happy....
Well, a bit happier.... what I'm not too happy about is all those bodge wires added by myself, and previous owners. You may have noticed in the chip replacement images above that I had already replaced some of those bodge wires with tidier repairs.... in my next post I'll cover what I did there in more detail, and tidy up all the other fixes on this board...