I have unhooked the ignition, so the ignition is being run by the stock ECU again, and MS is only controlling the fuel. MS is losing sync, which is all driven off the Cam and Crank position sensors. MS needs to see 24 crank pulses, then 1 cam pulse, then 24, then 1, and that's how it stays 'synced' with the motor. When it loses sync, it shuts off the outputs to be safe (so in this case, fuel) which is why you hear the hesitation. The sync error code I receive is 17 which means something like "wrong amount of crank triggers before seeing the cam trigger". Whether or not it's something in the hardware that is the issue, or a setting in the software, I am really unsure of. Support from the guru's are starting to fade little by little as well which doesn't help.
And here is a vid of the crank vs. cam square waves.
http://www.youtube.com/watch?v=kfUace3pZzM