Diagnose help

I have a 2002 mustang v6 I just recently changed over from a auto to manual. Before I started the swap the car ran great except the transmission slipping. Now I have made the swap the car starts up rough and if you accelerate it backfires like a ak47
 
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Just wondering. Did you re-use the automatic PCM? Have you made any tuning adjustments to the PCM?

Do you have an ODB2 scanner? Are you seeing any misfires on the ODB2 mode6 cylinder misfire data?

ForScan ODB2 scanner w ELM327 USB

Obviously one of the questions here is "is this problem caused by the swap" or "induced into the engine as a result of the massive amount of work done".
 
Yes I reused the auto pcm I have a manual pcm to go in just haven’t took it up to ford to get reprogrammed yet and i pulled all the codes on my scanner and that was 3 transmission codes for the auto and 2 for the o2 sensors which I don’t run rear o2 cause I have long tube headers and the she codes cause with the long tube headers it deletes the egr hole on the header so I deleted the whole egr system and the car ran fine before the swap stock motor btw no mods
 
Back fire is usually a symptom associated with timing. Are you positive that the correct spark plug wires are being run to the correct cylinders?

V6 coil pack wiring diagram

Back firing can also be caused by a cam sensor "issue". The V6 is very picky about the cam sensor. What can "cause" an unstable cam sensor signal? A bad alternator diode.

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The other thing that would be interesting to look at is what timing advance the PCM is using. I could see a case where the PCM is limiting advance because the PCM "thinks" it's still in park/neutral.
 
I’ll check my alternator tomorrow and see if that’s a issue and the wires are at 123564 that’s what I’ve seen I need to put them at I need that’s the only thing I took off when I replaced the trans cause I had to move the headers around to get it in and it was running right before we swapped it I changed out my coil pack no progress the cam sensors are original so I might be time to replace them