Puzzling one there...
I do know that the full-throttle auto kickdown will change the fuel injection parameters to the wide open throttle (WOT) fuel map (ignoring the O2 sensor). The A/C will smooth out the idle since it bumps up the idle speed a few hundred RPM.
Did you use an O2 "sensor safe" RTV to seal the intake manifold? Silicone and the acids in many RTV formulations can damage the O2 element.
I'd check to see if someone messed with the TB adjustment and check the TB sensor. I'd also check the coolant temp sensor, the fuel pressure, and the knock sensors. I've heard a collapsed lifter can trigger the knock sensors. There are also a few hoses under the manifold that tend to crack. If you had a bad boot, there's likely more damaged rubber hoses under the manifold. That rat's nest of heater & vac hoses is famous for causing trouble.
Pulling the AFM connector should permit the motor to idle, but will stall the motor if you touch the throttle. These cars have no 'limp mode' that I'm aware of.