I haven't had much time to look much further into the issue as we've had family over, and then a visit from the Flu... Joy!, but I've taken some time to do a bit of house keeping.
I've gone over the board with a microscope to check my work and look for any other signs of issues, everything looks good.
I did have some slightly odd glitching which seemed to change after things warmed up. This seemed to be related to the last few original sockets on the board to the CPU, and ROMS. I'd already tried cleaning and deoxit, so I have now replaced these and have a nice "clean" broken and glitched screen. So nothing related to our previous issues, but needed doing.
I also pulled the buffers at UD14 and UD13 (AB and BA lines) to test them as I traced a few of the failures on the basis of a power spike and UD14 was connected to 4 other failed chips. They tested Fine
I had already pulled and checked the buffers at UB4 and UB5 (ESD and BD lines) when I was initially diagnosing the issue that turned out to be failed SRAM.
This is what I know so far -
All ROMS read OK with a valid CRC. I had to replace two as they had failed, but I am currently only running the kernal, PETTESTER and Character ROMS, the other sockets are empty.
I can remove the serial and parallel controllers (UB12, 15, 16) and just run the CPU and CRTC and have the same issue.
The multiplexers on UD8, 9 ,10 - I replaced 10 as it was faulty, I also pulled UD8 as it's on SA0 and was corroded. It tested fine and has been cleaned and socketed. UD9 seems OK when looking at the logic so I have left alone.
The PETTEST memory test seems to run and pass. the screen is fairly garbled but you can see it running through and it never displays a fail message:

I cannot see, with a logic analyser, any issues with UD3, and a quick piggyback of a spare makes no difference. But I've not pulled it.
That's where I'm up to.