I just have the basic svtf stuff. Tune, orp, cai, and an exhaust. I'd really like to get a throttle body for it some day. I also drilled out the old tranny to subframe mount bushing and put poly ones in there.
On the stock tune mine had a slight hesitation until warmed up at a steady speed. The only thing I didn't do was clean the maf yet. I probably wouldn't hurt, but why would it run much better on the stock tune? I still think it has to be in the tune.