OK, getting back to the basics here and Ben's questions
"For example, how is your idle? Were you able to get the engine into ignition timing mode to set the ignition timing properly? How is cruising? How is WOT? How are throttle transitions?"
As you all can see I was unsure how to set or change the timing. The link to the timing guide was excellent to say the least, I had no idea about disconnecting the TPS and locking the timing, but I did have some hurdles to jump in order to accomplish this seemingly simple task.
So I grabbed my timing light, then realized that there are no spark plug wires to clamp to, tried the leads to the coil, this produced nothing so in a McGuyver way I made kind of an adapter using an old plug wire from a recent tune up on my Saturn
This allowed me to get the inductive flash to read the timing marks, so I thought.
This engine took most of my engine compartment and getting the light pointed at the timing marks, and to be able to see them was not working. I could see the backside of the pully clearly but the belt was interfering with my line of sight for the timing marks.
So I got under the car and hooked up a remote start switch so I could bump it around and have access to the pulley, then (McGuyver again) I put a small disk on my dremmel and using tape I carefully marked where the timing marks were at the front of the pulley, and created a new set of marks at the back of the pulley
Seen from the underside, (the last one is hidden in the shadow)
Anyway after all of this, warmed up the car, disconnected the TPS, revved to 3K a couple of times and checked the timing. It is currently set to 15 degrees advanced.
Still not idling well, but at least now I know where the timing is set, and how to adjust it.
I did run it around the block a couple of times hoping the computer would learn more, but still not idling well