Bad ECU? Do you have the knock sensor cable shielded properly? I'm guessing that whatever problem you're having with stumbling doesn't have to do with the knock sensor and is more likely a problem with a MAF sensor, etc. Have you got it tuned, and have you checked to see what your fuel pressure is? The stock fuel regulator should be able to regulate with an aftermarket fuel pump, but that's not necessarily a sure thing.

One other question: Did you just complete the swap, and has it always ran like this? Basically, is this a problem that just showed up after running fine for a long time, or is this a problem that you've had since the beginning?