All capacitors that I removed have been checked and the out of spec ones replaced. No change.
I started to remove more of the chips to test them (and put sockets in) and I got a bit carried away and removed pretty much every chip (except some RAM that I had already removed and tested). At least this means I can use my cheapo IC tester to run through all of the logic chips.
As a result, so far, I have found a faulty 74LS148 (U193 on the schematics). This chip is part of the interrupt control for the 68010 and drives the /IPL0 to /IPL2 signals. Having read through some of the documentation for the 68K series it looks like if this chip sets low on all three /IPLx then this initiates a level 7 interrupt which is non-maskable - I assume non-ignorable - by the 68010. Since the system then looks for confirmation on what the peripheral was that asked for the interrupt, I am making a leap that no peripheral responds and so the processor stops at the interrupt. Hence why the board starts to make the beep pattern for 'Main CPU timed out'.
I need to hook this 74LS148 chip up to a breadboard and see what the resulting outputs are to check if I'm anywhere close with this theory.
I still have a lot of chips to test that aren't supported by the cheapo chip tester. These are predominantly 74LS244s, 245s, 373s and 374s with a couple of 795s too.