So if you swapped the CPU, we can prob assume its a wiring issue, not board related.

If its multiple switches out, it also could be the opto board under the playfield (i think its a 10 opto on TZ) - the LM339s can go on this one as well causing a few issues.  Again, if you had another game with this board you could swap them and it would eliminate this as the cause or not quickly.

Otherwise, clean all the optos with a toothbrush to make sure there is no dust, and inspect the wiring looping from each one to see if there are any shorts