I had the same problem when I put a header on my kick motor. I dont see EFI sammys in CA very often, but I have dealt with many kick motors. I believe the idle system of the sammy is like the 89-90 kick. you have changed the air flow characteristics so the idle control valve or selanoids out side it normal limits. If it is like the 89-90 kick you can adjust the mechanical stop on the throttle plate. this will allow the vavle to be in the middle of its range. If it is like the later kicks, you dont mess with the throttle plate, but it has an adjustment screw to adjust the duty cycle.
I doubt that the TPS all the sudden went out of adjustement when you changed the exhaust. if O2 sensor is bad, i think that it would just go into limp mode, but weirder things have happened.
let us know if this works.