If I understand you correctly you just installed an aftermarket PCM. If that is the case then you need and autotap or a visit to the dealer to have your car go through a case learn prceedure. I know this is true is you change cam or remove cam sensor, but you may need to do some research and see when you need to have the car go through a case learn proceedure.
Retry your stock PCM. If the problem is still there, then check to see if you left your MAF sensor unplugged, etc. If the problem goes away with the stock PCM, then you should contact your PCM programmer since you may have a defective unit.
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