My friend is going to give me his unfinished Vintage Chip Tester kit. But if you think that is barking up the wrong tree ...
I think it is very unlikely the chip tester will help you figure out which chip to test, and you won't want to de-solder more parts than you have to, so IMHO that is not the place to start. But someone else may have another approach in mind... anyone?
A couple of other simple tests that may or may not give clues:
1) When you get error 42, if you "continue", can you boot into MacWorks and if so, does it operate correctly?
2) If you have a set of 3A ROMs + the video PROM for the square pixel screen modification kit... if you install those on the problem board, does it still give error 42? Since those don't have a serial number, error 42 would only be generated by a vertical retrace interrupt fault.
3) If you side-by-side compare the bad board with a good one, is there any visible evidence that the bad board has had any damage (repaired or not), or any parts replaced?
4) I don't know how much tolerance there is in the serial number timing, but I wonder if the crystal Y1 (near coordinates F1) was replaced with something not sufficiently close to 20 MHz... is it stuck to the bad board the same as on the good board?
5) The new 68000 CPU you installed in the previously dead board... if you put that CPU in the good board, it works and does not generate error 42, correct?
edit: added #5