I have a 2007 Grand Prix 3.8 N/A. I've been chasing a P0300 that's getting ready to drive me crazy. Changed the harmonic balancer and flex plate last week chasing down a knock coming from somewhere underneath. The flex plate ended up having 3 cracks in it. After getting the motor back in and going, It starts throwing a P0300 at highway speeds and continues down to lower speeds after driving a while.
According to my buddy's matco, all the misfires are occurring on 3 and 6.

Changed balancer and flexplate.
Changed wires & plugs.
Changed coil for 3 & 6
Changed icm.
Double checked ground wire to icm bracket.
Attempted a case relearn with matco maximus, but rev limiter kept me from hitting the 5150 RPM it wanted.

Now considering it is because i changed the balancer, and it needs a crank relearn, would i have better luck going back to my old balancer? Or any other advice?