Choppy Acceleration and wastegate under throttle..

[R Dubya]

I bought Richard Dunn's TGP in December and finally got the car here to me in NY just a few weeks ago.  I went through the process of getting the car back in running condition, PMIII, injectors, emptied fuel tank and replaced pump screen.  New R42LTS plugs and Delco wires, replaced the ICM module today because it failed the test at Advance.  Also replaced PCV valve, yet to do crank sensor, but I don't think I need to because I have good spark, and the car only has 38K on the clock.

I have been trying to get this thing running right, and I thought I had it fixed with the new module.  This is not the case however, because when it idles, it idles great, no misses, and it sounds strong.  A lifter was sticking badly when I first ran the car, but with treatment and light synthetic Mobil 1 oil, that went away.  But when I hit the gas in drive or reverse, the car still has a choppy idle, and when I accelerate, I can hear the wastegate releasing the boost.  I am running the Jeff M TG160 with thermostat, and by rights, this thing should be tearing ass, but it's still giving me problems.  What are the chances that something is internally wrong with the wastegate?  How about the actuator?  I have already changed the boost controller with the one from my higher mileage TGP, it seems to make a slight difference, but this choppy accleration is still hanging around.  

I suppose there could be something hanging up inside the heads still, but the idle is right, but after a rev, it stays high for a second and then slowly lowers to around 1000-1200 rpm.  But under accleration, I can hear a flapping or flutter sound from under the hood.  

Does anyone have any input to these issues I'm having?  I'm fairly sure this is a boost related issue, and I'd appreciate any and all tips.  Thanks.