2006 GT supercharged HELP

Hello everyone.

Can you please help? I don't want to scare anyone away with a long story...so there is a short one and a long one.
The short story is the following:
2006 Mustang GT Supercharged with a S-Trim Vortech liquid/air blower system. Other performance Mods include aluminum drive shaft, 3.73 gears, 39lb injectors, X-Pipe exhaust with flows.
....surging of vehicle and unsteady RPM...as well as loss of HP. (less than 230 with blower) Diagnosing and replacement of some sensors and coil packs has been with no results. Got any suggestions on what it could be?

The Long story is the following
I have a "stuttering" issue that can't be resolved. Last year when the blower was installed, it ran great and plenty of power. Then 3 days later...the belt shredded and grabbed the nearby wiring harness, shredding and tearing the wires. Belt was replaced, wires were fixed, but there has ever since been a surging issue with the cars performance. At crusing speed, it intermittantly surges. On acceleration, it doesn't perform well at all. When in neutral, if you rev the RPM to anywhere around 2-4000, it pops and sound like crap. I have been driving it anyways because it is still driveable I just don't really get on it.

The following parts have been replaced: Coil packs, upper and lower cam shaft position sensors, new HT0 plugs. Tune has been re-tried. The intercooler could have been the problem as it was thought it was leaking water into the intake (defective) But with no water in the intercooler at all...the same thing occurs.

It now runs even worse than after the intercooler diagnosis was made. The tune was messed with, and then gave up on so it runs horrible. I am going to take it to a different shop and see what they can figure, but its going to cost bucks to diagnose. So I figured I would give some good ol' Stangnet people a chance to see if they can provide a possible solution.

Can anyone think of something that may be wrong? Possible solution direction to strive towards? Bad wires or maybe a sensor gone bad? Fresh new tune maybe? How about maybe the injectors? Or is it really the intercooler? What do you think?
 
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Sounds like the problem all started with the shredded belt tearing into the wiring harness, so I would start there. Was the harness section repaired or replaced? If it was repaired, try searching for a short between wires inside of the harness.
 
Sounds like the problem all started with the shredded belt tearing into the wiring harness, so I would start there. Was the harness section repaired or replaced? If it was repaired, try searching for a short between wires inside of the harness.

Thanks for the reply Anthony! The wires were repaired by an expert wiring tech and the wires were all tested for any voltage fluctuation and none was found after repair. Maybe it shorted something that has to do with those wires causing it to permanently malfunction is what I am thinking. Question is...what? 4wires were completely severed and one was frayed real bad. The wire leading to the Mafia was severed...and repaired and a new Mafia installed.

So many possibilities. What would be the typical causes of an RPM fluctuation?
 
Here is a thought. Maybe it is unrelated to your belt causing damage. Maybe the timing is coincidence. I remember having work done on the sn95 I used to own, and my car started to stutter on acceleration like yours and do the same on idle as yours. My self and my mechanic could not figure out what was wrong. Everything tested normal. One day as a last stitch effort he suggested that we change the sparkplugs, I told him that i had replaced them 6 months earlier with some platinum plugs but was willing to try anything at that point. We changed the plugs and the car ran perfectly. Upon inspection of the plugs they all looked fine. When he hooked it up to his computer before we changed the plugs it did not register that their was a problem even though we could both clearly see a problem. Sometimes it is just something simple.
 
Here is a thought. Maybe it is unrelated to your belt causing damage. Maybe the timing is coincidence. I remember having work done on the sn95 I used to own, and my car started to stutter on acceleration like yours and do the same on idle as yours. My self and my mechanic could not figure out what was wrong. Everything tested normal. One day as a last stitch effort he suggested that we change the sparkplugs, I told him that i had replaced them 6 months earlier with some platinum plugs but was willing to try anything at that point. We changed the plugs and the car ran perfectly. Upon inspection of the plugs they all looked fine. When he hooked it up to his computer before we changed the plugs it did not register that their was a problem even though we could both clearly see a problem. Sometimes it is just something simple.

I had a similar thing happen but with me it was the plug wires. The dealer had the car and ran every test they could think of to no-avail. My brother in law drove it around the block and said "plug wires" They had checked them at the dealer but my brother in law was sure. So I replaced them and that was it.