Have you made sure the TPS is properly calibrated?
Well, the O2 sensor is easy enough to check... unplug it. It's just a trim sensor, but the ECU is allowed to add quite a bit based on the O2 sensor's feedback.
Recheck the vacuum hoses. As silicone is non porous and rather slick you should use clamps or sip tied at every connection to be sure none leak or blow off.. I had two which just refused to stay on.
When adjusting the timing I trust you had the diagnostic jumper in place.
Does the idle issue occur both in park and in neutral? I don't know a whole lot about automatic transmissions, so I'll leave this to someone else.
Have you tried to clean the AFM at any point? The AFM is VERY easy to screw up by 'cleaning' it as it is an optic device... most cleaning agents will fog the lenses and sensor. you can unplug the AFM and see how the car runs as well, but I don't think the AFM is likely.
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