Just throwing this out there... I can flash PATS keys from scratch if you need it. I need two keys(proper keys for the model year, 99.5+ keys will not flash to a 98-99.5 PCM), and the PCM. Also, I'd need the milliage of the car, and the VIN#, this way, if you do swap ECUs you'll pass a VIN-Ver if you need to for emissions/registration. The PCM would end up getting the latest software available. I.e., an SFG0 would get updated to an SFG2 (or 3 can't remember which is latest, you get the point).
I'd do it for the cost of a temp subscription to the FEPS software I need o do the flash. Costs like $35-45 or so IIRC. And If I can't make it work for some reason, I'd refund.
About your issues... Does it idle smooth, and stay around ~750RPM? Are the fuel injectors still the oem EV1 style (has metal retaining clip)? If they are the EV6 newer style(has less bulky connector), the plastic clips break just by looking at them, and you may have a poor/loose connection.
does your scan tool show Live Data while the car is running? Can you look to see what the LTFT is for both banks, and watch timing, O2 Voltage etc. to try and glean some info about what the issue might be? If you need to, take a video of the scan tools Live Data, and post it.