custom designed stuff is super hard to diagnose. this might be a bear to figure out due to the obfuscation of many parts and their functions. going to be super tough since a programmable chip with unknown functions has been implemented and how it's SUPPOSED to act is unknown, since we have no working model to compare against...
to begin... any chip that shares those control lines with the other chips could be the culprit. not just the PLC. any chip could be at fault and holding the lines hostage... causing it to lock up.
for instance, a bad ROM chip with a locked data line could cause the datalines for the ram to act weird and show up as bad ram in a system test, or even cause the CPU to not boot all the way, even though they are actually fine.
since it's both of those lines, id' suspect any other chip that also uses those 2 lines... but wouldn't discount a chip that uses just one, since it could be in control another chip down the stream that uses the other line... causing them both to be locked up high.
try dragging one line or the other low with a 10k or even a 1k resistor tied to ground and see what it does. see if dragging one down causes the other to start acting normal. could start pointing you in a direction to start searching.
good luck!