Help!! Changed Clutch, Now Stalls And Idles Up And Down

Hi. Im brand new tothe forum. I have a 96 cobra superchipped for 35 hp and removed rev and speed limiter, k&n cold air intake with stock maf, bbk high flow cats h-pipe with side exhaust, hurst short throw shifter, 3.73 with t-lock, was planning on supercharging it very soon but plans just changed so i took out the stage 3 clitch i had installed last fall. I dropped down to a stage 1 this weekend and it went flawlessly until i finished up and started the car to get it off the ramps. The car turned over fine and then started and made a puff of exhaust then died. I chwcked everything out and it all seemed good. All hoses and sensors were hooked up but the right exhaust pipe wasnt seated on the manifold correctly i started it again and it was fine. Clutch is perfect short tight travel and engages very well. I drove easily around town truing to break it in and when i came to a stop light and had the clutch disengaged the car stalled. I strted it back up an drove it a mile home. When i got home the car was aluggish and was idling up and down between 800 an 1100 rpm harmonically. Does anyone have any idea what is goin on?!?! I cant track it down. Te exhaust still has a small leak on the passenger manifold im going o take care of tonight. I drove it 3/4 of a mile to work and it didnt stall or idle funny.

It only died after startup on tht very first start. Now, it starts fine and idles fine until it warms up then it will die if i come to a stop and have it in neutral or have the clutch pushed in and it sits at a complete stop for roughly a second. It will idle down then die 50% of the time an the other 50% of the time it will idle up and down between 500 and 1100 rpms. I did have to jack up the front of the motor about 2 inches to get to the top 2 tranny bolts so i couldve stretched a vac line but do u think with the exhaust leak my o2 sensors could just be reading all messed up? Im going to fix the exhaust leak an check the vac lines after work but my diesel is also tore apart so i had to drive the cobra to work today. Any other ideas for things for me to check? I dont believe an o2 sensor would cause it to die but certainly the erratic idle ??