So, I did the swap, just put another 3.8 in it. I put everything back together and fired it up and I have a pretty bad misfire... it is throwing a cylinder 1 code... I replaced the plug and wires during the swap and I again replaced the #1 plug and wire to see if it would help. It was still misfiring. It has a slight misfire when idling but gets really bad when under a load (even the fan kicking on can cause it to misfire worse). However, when reving (after a slight hesitation) it clears up and is definitely hitting on all six under high rpm .... One thing I was thinking, is that one of the hats on the fuel injectors fell off when pulling it out of the intake so I went and bought a new seal kits for all of the injectors... This came with the O rings and hats. The hats had a slightly smaller diameter opening than the old ones. I took them back and they told me that it was because they were aftermarket and that they were not blocking the injector jets so it should be fine. I had them double check that it was for my car make and even went to another store to check the part and they were the same at the other store... plus I put them on all of the cylinders instead of just the one... why would it only throw a code on one of the cylinders.