Hey brother, I'm a 97 Gt owner myself. Pi swap cars run just fine without a tune, and most people don't get a tune unless the have seen other work do e at the same time. I know that the diagnostic codes say the O2's, but how you're describing the problem sounds like that's what it is. Sometimes it's just that simple and some other times it will tell you something totally different from what is actually wrong, like let's say a good ole' vacuum leak. But that's not your problem. You definitely need to dive into the O2 sensors problems and make sure everything is plug up correctly, and give it a once over. Was there anything wrong before you swapped?
No problems at least anything that was throwing a code before, same exhaust as before the swap too, could the o2 sensor be the cause of the misfiring symptoms under low rpms and full throttle?