Possible timing problem

The ignition timing is PCM controlled and would advance or retard according to conditions.

For every revolution of the camshaft, there must be 2 revolutions of the crankshaft therefore it is possible as you mentioned that the piston is at TDC of exhaust instead of compression but the camshafts would not lie to you. IF both camshafts are lined up correctly, it does not matter as the TDC would always be correct.

When turning the crankshaft to check the timing chain timing, did you turn the crankshaft clockwise? You cannot turn it anticlockwise as that can result in the camshaft timing going off due to slack of the tensioner.

For PCM relearns, generally you need not do anything except run the vehicles. Some highway driving then to town for a few minutes and back to the highway and the relearn should mostly complete itself.
If engine is only running on 4 cylinders, it could be otoer things that is causing it. Ensure the spark plugs are working, injectors etc. Get a compression test to determine if they are within specs.

Check for dislodged vacuum hoses and clean the throttle body if necessary.

Misfire monitor would not work if the the Adaptive Numerator has not been relearned. The Adaptive Numerator is updated by the PCM for every key-on and is relearned after battery disconnect.

Replacing one head will most likely give you different compression on the 2 banks, that is, one head new, one with miles.

As I said before, no re learn for the timing of the motor as KHL said.

Roy

Compression pressure should be between 170 to 225 psi and as Roy mentioned, they could vary with a new head but variation should not be more than 10 percent.

The pressure might tell us something if they are out of range.