I also feel your pain, it is frustrating. I also agree on stepping back from and playing with a fun project to clear your mind.
Then I would start over as if it were a new problem. Since it ran good with this combination for a little while I would first check the feedback side of the system, the oxygen sensor. Try unplugging it, doing a hard reset on the ECM, then start it up and see what happens. This should put it in open loop and if your base programming and wiring is mostly correct it should run pretty good. If not you are chasing a ghost can be difficult to find. It runs good you are looking at something in the feedback either the wiring or your new oxygen sensors.
Remove the fan belt, hard reset, then retest. This will eliminate alternator AC voltage and, believe it or not, problems with static electricity building up the belt itself (I have only seen this issue one time in 40 years being a professional mechanic).
You could have a bad sensor failing when hot, ie. CTS, TPS, or even PCM. Test, don't just replace. I have seen a lot of new parts, counterfeit factory parts, and even new factory parts are bad right out of the box. Remember "NEW" means Never Ever Worked.
If it still runs poorly, I would then look at the wiring, doing a load test on each individual wire, since it seemed to run okay until you mounted the PCM. Wires can pass an ohmmeter test and still not be able to carry the amps necessary to do their job. I use a regular halogen headlights bulb (5 amps) that I have wires attached to it to check small circuits up to 16 gauge wire.. DISCONNECT PCM. Disconnect both ends of the circuit you are working on, this includes every connection that branches off of the circuit. One lead goes to negative battery terminal and the other goes to one end of the circuit you are testing. You then take the other end of the wire and touch it to the positive battery terminal. It should light up the headlight bulb brightly. Repeat on the other branches of the same circuit.
If any circuit fails the above test, then you're going to have to inspect the harness going as far as stripping off the loom and tape and checking each individual wire physically, even tugging on the wire, I have seen the conductor broken inside the insulation.
Good luck, Jeff
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