msm650

I recently swapped in a used engine into my 2005 MSM and have been having issues getting the base timing set. Right now, the car will not start unless I put the offset at 180 degrees. If I have it at or near zero, the car just backfires very badly while trying to start. The car idles okay when I have the offset at 180 degrees, but the timing when checked with a light it nowhere near 10 degrees advanced when I used fixed timing (it is significantly retarded). I try increasing the offset and the engine starts to sound like it is knocking so I shut it off. The offset doesn't seem to make much difference in the timing even when fixed.

I am very confused as to what is going on since the original engine in my car only needed -4 degrees for the offset to set the base timing.

Things I have checked:

1. Crank trigger wheel orientation
2. Timing belt installing (I replaced it before swapping the used engine in)
3. Coil pack connectors on the correct coil packs
4. Crank position sensor gap

Is there something that I installed backwards? I am not sure how to trouble shoot this other than putting the stock ECU back in to use for codes.

Current Ignition settings:

Spark Mode: Miata 99-05
Ignition input Capture: Falling Edge
Spark Output: Going High
Number of Coils: Wasted spark
Cam Input: CMP

Thanks in advance for the help.