[Hozer 88GTConv]

Have you run a cylinder balance test with a Actron code scanner?
I'd do a KOER test after it is hot and exhibiting the symptoms you are describing and then follow it with a cylinder balance test.
It will identify a weak or weak cylinders and should really help you eliminate much of your troubleshooting considerations.
I'd also talk to your longtube vendor and see if they have heard of probs with 02's at those locations not providing temp readings within the range of OEM 02's. A voltage calibration may be necessary...
good luck...