Idle/ gas problems wants to stall

I recently removed my Vortech SC for a Roush trubo kit. for roughly 1 month before I removed my SC it started acting really funny. I would sometimes start up my car either in the morning or after driving it for a while and it would want to stall, it would sputter, my rpm would bounce from 100-700 until it almost dies or dies. I would turn it off and turn it back on and 90% of the time it wouldnt do it on the second start.

Now, I have my Roush kit installed, and I have the same problem. These are new injectors and a new tune, so it couldnt of been any of the two from the SC. The funny thing is, when I go in reverse, it really sputters, sounds like its bogging down and kinda wants to stall. After goign in reverse, forward motion seems just as shitty for the next minute 50% of the time. Once I have been driving and continue to drive, it doesnt do this at lights or anything, I have replaced the upper O2 sensor with a Bosh as well.

A buddy of mine told me to ask Ray so, if your there Ray, I would appreciate your opinoin.

ever had your fuel pump replaced? it should be under recall. im just guessing though.

It was replaced, a couple years ago before I ownde dthe car, its in the car report through ford under my vin. Now, i am really concerned, i was driving it today and had an ever bigger problem. I went into walmart, came out, started my car, let it idle for a min, then drove off. I gave it 3/4 throttle to get into boost through first gear. I stopped at the stop sign and was going to take a left, but I heard a whole shit load of clunking noises, and vibrations. I think it may be my tranny and but you tell me what you think.

I installed my FS lightweight flywheel a long time ago, along with a Spec stg 2 clutch. After that, my tranny was VERY loud when the clutch was drepressed and the car was ust sitting there at idle. Its very chattery, VERY. I installed another LW flywheel of the same type on me buddy's car and it had no chatter, very very little.. He mentioned it was prolyl my tranny. Then, I installed another LW flywheel and clutch in my other buddy's focus and it also was quite...?

I have about half the chatter as when im at idle when im in gear driving down the road. And considering my reverse is ALWAYS clunky now, it studders and makes it seem like the car is gonna die, then it runs bad from there one for a min most of the time as I said above.

Now here is the think, there is another problem. I borke in my turbo for a while on regular 5w30 oil for 500miles only running to 5 grand and half the time into full throttle and boost. After that I went to checker becuae they gave me a belt that was too tight, it had to be forced onto the pulleys and the tentioner was all the way maxed out. After I took off that belt and replaced it with a larger sized belt, I heard a noise, it sounded like an exhaust leak, prety deap, sounded throaty, and the car would not run right.. It is starting to happen more and more as it happed for me right after the above with all the noises at the stop sign. But, when I gave it full throttle, it cleared up slowly and went into 4-5000 rpm and into more boost. Then it ran fine the rest of the drive home.

What do you guys think it could be?

Leak in turbo assembly somewhere?
Tranny on its way out?
Fuel pump going bad?
Fuel Filter?
Engine problem, out of ballance (due to too tight a belt or somethin) piston problem etc.?
Tuning?

Thing is, I have an Xcal 2 being ordered and im going in for tuning this thurs. I do not know what is wrong, and the idle/ sputter and want to stall issue had been an issue for a while when I had my SC installed. I really would like to identify the problem so that I may fix it. Thanks a TON guys

Yes, replaced it, but I used stock cause I messed up the one Spec sent me, I used a brand new Ford unit, though.

Edit , well, it happened to me again, I replaced the fuel filter and drove it around. I got kinda rough on it, but only to 6ooo rpm into full boost and it happpens when going from first to second gear. As soon as I get into second, it starts doing it. You can totally hear it in the exhause, its like the turbo is spinning differently or something.. It goes from a smooth sounding idle to a VERY lumpy, aggressve idle, almost like a v8, although, it doesnt try to stall.. It stays at a p erfect idle. And the car is a DOG, no power whatsoever.
Yet, it clears up after I turn it off and back on and drive if for about a mile or so. The Reverse problem with it totally sputtering and being doggish continues too. This all started after I took off a serpentine belt that was entirely too tight. The Tensioner was maxed out and the belt had been forced on there. Once I removed that belt and threw a larger one on, it started doing all this..?? Im still unsure on what it could be but it needs to be fixed before I take it in to get it tuned.