Good to hear from you. I thought I would pass on just a couple of thoughts which may or may not be helpful. The intake manifold has a vacum actuator to switch from long to short runner. Is this effected by boost? Any other issues that can be cuases by boost in the vacum system? brake booster etc.? It might be easier to tune if you move the MAF to the intake side of the s/c. Also Ken Rudy of Dyno-Comp (formally of Renntech) is tuning for superchargers without the use is the AEM. He is doing all tuning in the stock ECU and has taught the stock ECU to read boost. I hope you are successful as you break new ground. I know first hand what it is like to be pioneer/guinea pig as it took over a month to get my V8 to fire up after installing it.