P0205, P0300, P0303, and P0305 codes: What should I do?

Sounds like a tricky one, it's tough that the problem duplicated and didn't follow like you had hoped. But yeah, at the end of the day, the codes mean what they mean from the PCM's perspective. In this case, if the wiring, connector and injector are indeed good, then my next guess would be an internal PCM circuit issue.

Another thought...not sure if it has merit or not. The connector for injector #6 could be damaged and caused a second circuit fault in the PCM when you plugged it into #5. I would not think this is very likely or common that this happens, but perhaps it is possible if the wires were fused.

P.S. If #4 is also not firing, but not giving any codes, something very odd is going one and I start leaning more towards the PCM.
I put in a PCM from a '01 XJ. It started great and ran all 6 cylinders but eventually gave a manufacturer code (expected) and a few oxygen sensor codes. I turned off the TJ to clear the codes and restarted, and it gave codes circuit malfunction codes for 5, 6, 1 and 2. Point is... it doesn't look like there's a problem with the injectors or wiring. It's looking like the PCM.
 
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I'm 'driving' it to the mechanic tomorrow. Hopefully they find some faulty wires that I somehow overlooked ad I can just run some new wires. I swear to christ every time I'm about to go out of town this Jeep starts misfiring or the computer goes out.
 
Still working on it. Two mechanics said it was the PCM. Sent it to SIA Electronics to be repaired. They replaced drivers #4, 5 and 6 and said everything else checked out. Installed it today, no change. Not sure if injectors 4, 5, and 6 are still not working - I can't keep it running long enough to unplug one and check it.

So I'm sending it back to SIA Electronics, hesitantly. Then I'll either send it to Flagship or the manufacturer to be repaired, again. (Flagship doesn't sell my specific computer. A dozen others for my year TJ, but not mine.)

It runs for a few seconds and shuts off.
It will 'run' if I keep my foot on the pedal.
It drinks gas like a sailor.
The cluster is flickering like it's having a seizure.
It's giving b0 and b8 'codes'.
The left headlight and fog light do not work.
When I turn on the headlight(s), the cluster does not light up.

Individually I'd be looking at the multi-function switch, injectors, Idle Air Control Valve, Crankshaft Position Sensor, loose instrument panel connection, etc etc. But since the PCM did indeed need 3 new drivers and a bad PCM could cause all of these issues, I'm still leaning toward the PCM.