gutless wonder

I have a 89 Daytona Shelby 2.5 T1 with problems,

#1. I did a auto to 5-speed conversion, I have a 2.2 computer for it but when i hook up the scan tool to this thing it still thinks its a 2.5 t-1 auto, I am guessing there is another module I dont know about that determines this. What do I do to change this.

#2. The car will not rev over 4000 at all. will not do it anytime, checked cam timing, good fuel pressure, good spark, new pick up coil, no play in dist. shudder wheel. Possible knock sensor problem? There is no change when changing ecu's. dist timing is set a 12 deg. Air/fuel looks good at all times. the car has a open 3'' exhaust makes alot of backfiring and popping on decel dont know if thats normal or what, no one around here has a turbo dodge so i have nothing to go by.

#3. Car only make 5psi without air bleed on wastegate, took the car to the track ran it twice once with 10lbs and once at 15lbs with only a .06 gain.

I am assuming that 2 and 3 are related, no codes are thrown.

Any ideas?