Hesitation problem,
 

2001 Mustang GT 'vert 4.6 2V. Hope someone can help with this. I just had Auto Logic chip changed for SCT Tuner. Changed to C&L Plenum & changed C&L MAF for 90MM lightning. Running 8lbs. boost with Paxton Novi 1000. Making 365rwhp, but have an annoying hesitation problem at approx. 2,500-3,800 RPM. If I put some gas to it, the hesitation goes away. Before changes and recent dyno tune the problem was even worse. I have tried just about everything to resolve this, but no luck so far.
Please help, I have a bunch of hard earned $ in this car.

I have been to the mountain-top and I have seen the promised land. I had a dream today that I was riding on a purple dinosaur... eating ho-ho's with George Wallace. And the loooooorrrrd himself spoke unto me a message for you, <Gawd voice> "Get thee to a dyno tuner before you blow something up! And quit touching yerself."</Gawd voice>

since you changed to a 90mm MAF you're definitely going to need some custom tweeking of the MAF xfer table. I always hand curve that. Do a run, adjust, cool down, repeat.

What kind of throttle position and what gear are you in when the problem occurs.

I just had it dyno tuned Saturday. The tuner can't seem to tune out the hesitation. I have had Chris Johnson tune it the time before and he couldn't get rid of it either. The throttle position is only partially open as in city street driving. It seems to be worse in 2nd gear. The reason I changed out the C&L maf was under the recommendation of the current tuner. I purchased a 90mm maf from an '04 Cobra along with a billet adapter and a rubber plumbing reducer for the transition from 3 1/2" to 4". Seems like a waste of time and money to me, but I don't tune Mustangs for a living. The car has stock internals with 22,000 miles. The first dyno pull showed only 317 rwhp. The original S/C install was 368 rwhp. I have no idea how I lost 40hp. the tuning conditions were similar. (temp, humidity, fuel; etc.)

Has anyone touched the MAF since the original 368 tune? In any case, post up a pic of your underhood. I need to see a few things.

quick tip:
One old trick to get MAF readings to stabilize is to tinker with the clocking of the MAF body. Sometimes they're sensitive in that way and a little twist one way or the other will help.

Also... I don't care how new they are, check your plugs and post a pic of them up close at the electrodes.

We're definitely going to need several parameters datalogged including things like timing, maf counts, stft, ltft, fuel pressure (if you can), A/F ratio and some reading of calculated load, and rpm. Your tuner should know how to log those with your Xcal2 and a laptop, or he should have the ability with his own systems. That'll be the path to understanding what's happening so you can tune out the glitch.

Last time I saw such a problem (specifically on a blower car) it was a corrupted tune, so perhaps he should start over with a spanking new tune and quit horsing around with one that he can't seem to get spot on.

Hesitation Problem
 

Here are pictures of the engine. Let me know if there's anything else you need images of. Sorry for the delay in getting this to ya , but work keeps getting in the way. The C&L MAF was replaced with a 90MM Cobra/Lightning MAF with an adapter from VMS. The original tune was done using an Auto Logic Chip. This last tune was done with SCT tuner programer replacing the Auto Logic Chip. The plugs were removed, inspected and gapped at .035.
The TPS was tested with a volt meter and even though it was ok replaced with another TPS. The bypass valve was checked and it's fine. Now the tuner wants to replace the coil packs. Wouldn't an ignition problem shown up on his tuning software?

very off topic i know, but in ur first pic, in the top left corner. what type of mustang is that?

Hesitation Problem
 

1965 Mustang GT, HiPo 289 built to GT350 specs, Top Loader 4spd., 3:55 nine inch.