Wow, you are tearing up Saudi Arabia in that hopped up 94! That is just too cool.
As for your problem, it has to be wiring or computer related as the clutch should have no effect on your Idle speed. When you disconnected the IAC motor, it probably defaults to a specific setting, thus curing the stalling problem, this probably sets a Check engine light.
Most likely the new 80mm MAF install threw something off, their calibration may not be working properly with all the modifications you list, of course they will blame something else first, like your wiring etc...
I'm a Ford Rookie, so can't add too much more
------------------
Frank W
90 5.0 LX coupe Daily driver. Silencer removed, K&N filter. Flexalite fan, 3 core radiator. FMS flywheel and Clutch
88 Notch 2.3L 5 speed Parts/beater car
74 Chevy Laguna Type S-3 305 fixing soon, getting a 454 to put in garage
www.chevellepages.com/folingo