My 02 Gt was doing something similar. I replaced the front 02's with Bosch sensors and then a few months later the car started running bad. I have an A/F gauge in the Drivers side exaust pipe and it was reading ok and the car would set the CEL but it would run like hell. I finally decided to replace the passenger 02 sensor with a Motorcraft unit and voila it's fixed. I have yet to replace the drivers side 02 sensor but it is on my list of stuff do soon. I am speculating that the passenger side 02 was reading incorrectly because there were a few times that I got a misfire code from Bank 1 running too rich that it was trying to foul the plugs on that side and then the drivers side bank ran perfectly. I am not saying this is your issue but if you aftermarket 02 sensors then you may want to look in to it.
Thanks for the input. But it has new Motorcraft O2 sensors in it now. Along with a new motor, and it runs beautifully. I never did get a definite answer about it, but my issues have since been resolved.