Help Diagnosing Slew of CEL Codes

[blue62]

Well with the timing issue resolved your making progress.
The ill running when warmed up is kind of a mystery.

It would be interesting to have a scanner hooked up to it and see if it begins to run poorly right when it first goes into closed loop. or not.

My first thought was a possible bad MAF sensor but lots of times you see the engine hunting at idle when cold. With a bad MF.

Another thought is:
What readings is the DME getting from the coolant temp. sensor after the engine has been warmed up.
If the coolant temp. sensor is showing cold or low temp. when the engine is warmed up then the DME will still be on the cold start map.(rich in fuel) even though the engine is at operating temp.
If that were the case it also would probably not go into closed loop when warmed up.
May be something to look at.