Changed Motor in 96 Intrepid now won't run right?

Hello, I bought a 96 intrepid and it was supposed to need timing chain, but ended up being blown up, so I took a motor out of a 94 intrepid that I had and put into the 96. They are both the 3.3L, and now it is backfiring really badly and acts like its running on 4 cylinders then it will quit backfiring and have full power. While it is backfiring if I put it in neutral it will rev up just fine with no backfiring but as soon as I put it back in gear it starts doing it again. I talked to chrysler and they said with going to a 96 from a 94 I should've stripped both motors down to just the block and heads and swapped everything from the 96 motor and put on the 94 motor. I have a reading from the check engine light that says an Oxygen sensor is bad. I took the 96's Oxygen sensors and put in and it went about 4 miles with full power then engine light came on again and lost power again. Any suggestions or hints? Please help I'm getting very frustrated.