I have a 03' with 2.2 swap and ap1-ECU.

I drove an hour to a resturant in tampa got there ate and left an hour later as soon as i started the car it threw a cel i stoped at advance and ran the code it threw #4 missfire P1399. Car runs fine no problem what so ever no knocking missing etc.

Any ideas?

 

P1399 is a random/multiple misfire.

I'd suspect you are borderline lean with the 03 ECU.

00-01 ECU is the way to go with the 2.2L.