Thanks for the help.
We are having issues with bucking/bogging down at low rpm. Getting misfire codes on all cylinders. Car feels great on the highway. Gets great highway mileage. Around town it feels lousy, stutters, bucks, rough idle, rough acceleration.
Like I said before, I've read the threads. I know that these symptoms can point to a dozen different problems. I know that this problem is more than likely not engine specific.
A mechanic told me yesterday that the gear that turns the cam shaft is likely a few teeth off from what the ECU thinks it is, and that's causing timing issues in a closed loop. I wanted to call BS because I thought the guy who swapped my engine swapped the ECU as well, but I realized I don't know. That's when I decided I probably needed to find out more about exactly what I have before I could solve the problem.