So the +12V, -12V and +5V go out when you unplug the after market supply. OK, sounds good, the +5VI and the +18V LED's ( the outer 2 ) on the top board are generated from the PDU board under where the original lower power supply would be, so they would stay lit.
The dotmation display and control board would still be powered by a supply up in the top box, OR the after market supply is also suppling the voltage up to the top box for the dotmation stuff. That's OK if it is wired like that, it can be done.
If the comm cables are good, as suggested from above by PLAYKLAX01, I would still suspect the problem is with the power supply(s). Even though the LED's come on, that does not mean the voltage is 'correct'. Meaning - you need to check the ripple AC on the DC voltage. The AC voltage reading should be below 10mV, to maybe as high as 20mV might be OK. ( on a digital meter it would be .010 V ) Anything higher would mean the capacitors are bad, usually when new capacitors are installed the AC ripple would be pretty low, < 5mV. As the capacitors go bad the AC ripple goes up. This is basically noise on the DC voltage. When you are talking about suppling DC voltage to computer chips and communication chips, this ripple/noise can look like signals to these devices. Thus causing intermittent problems or just plain won't work.
You suggest your problem may be in the main power supply. If you mean the PDU board, as I mentioned before, then change the 5 capacitors on that. I fixed my machine not powering up by replacing those. They are just as important as the power supply capacitors, maybe more so as the +5VI is for the I/O board devices. It is used for the communication devices.
Tony