OK, so it's been a while, but I spent a little time looking at this machine today and voilå!!!
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It's fully working again including floppy disks and the additional 24K of RAM:
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The culprits being these two buggers:
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The 74LS04 being U16 and the 74LS138 being from U22.
It's entirely possible that their demise is related to me over-volting the board (8.5v rather than 5v) ages back when I was first building it, and that might hint that more may die down the line.
And before anybody says "those white dots don't indicate pin 1, did you plug them in backwards" no, that's not the case, that goes back to a previous issue when I ended up removing all the ICs and testing them, the white dot indicates they were tested and at the time, were fine. They aren't now.
Nevertheless I didn't have the parts to fix it at CL4. Perhaps it'll work at CL5 :)
In the meantime I'm just happy it's alive again.
EDIT - nearly forgot to mention, I found the faulty chips using my thermal camera as I wasn't getting very far with 'traditional' troubleshooting methods.