I think I may have solved it! I had a buddy come by to give me another set of eyes and a clear mind.

First we jumped the CHT sensor at the connector to warm it up. Then once it was warm we pulled the jumper to see what would happen. When I did, it died as expected.

Next I jumped it again and unplugged the AFM. It started running very poorly.

Then I plugged everything back in and started it, it started up well and idled a bit high at 1100 RPM. But, if I started to press the throttle in I could see that as soon as the idle switch disconnected the car would die. I did my best to make sure the switch had as little play as possible before the throttle started to open. This seemed to help a bit but it would still flood and die.

Since I was unplugging other sensors we decided to unplug the WOT sensor and try starting it. All of a sudden it idled better and I could disconnect the idle switch and it wouldn’t die.

So, I took the cover off the WOT and could clearly see it was making a connection even when the car was at idle. Someone had definitely messed with it and bent the upper arm so that it was in contact at all times.

My buddy gently bent the arm back and we dialed it in so it would only come on at full throttle. We revved it a few times, and every thing continued to work great. We buttoned everything up and took it out for a drive.

The bucking out of first gear was gone, it no longer had any dead spots when under throttle. It just pulled hard all the way up.

I have it in the garage now cooling down. My last test is to cold start it and hope it doesn’t die.

Great progress! The full-throttle mode ignores the AFM and uses preset fuel settings. Also, when the idle switch is closed
and the full throttle switch is grounded, the DME ECM goes into the idle setting mode, which prevents idle valve from functioning.
You need the idle switch to function or you'll have a very low idle (or no idle) with a cold engine.

The key problem, related to full throttle switch, would have been determined sooner by using the recommended ICV test procedure
in post #55. The ICV test would have indicated that the ICV was non-functional, because it was in the idle setup mode with the full
throttle switch at ground with the idle switch.

To bring some closure to the thread. The car now starts well when cold.

I would be surprised to see others have the same issue I did, as the Full Throttle sensor had to have been bent to be in contact at all times. Hopefully all of the troubleshooting info in the thread will help someone find their problem faster.

I do still want to properly tune the car to ensure its running in top shape.

The one thing I would be curious to know is why would someone modify the Full Throttle sensor to be engaged at all times while simultaneously adjusting the bypass screw on the AFM to be full rich? Is there a situation where that would be beneficial? It seems to me like it would only create a situation where the motor flooded every time you started it.

Are there people out there doing this and then just developing custom tunes on their chip to compensate?

Congrats !

Yep, the OP did something to the engine i.e. adding a "cheap" fuel mod hack to make it run rich all the time, not good for the engine ... which was why I recommended reaching out to the fella for more info earlier.

Good find.

Now that you fixed the WOT switch you really need to set base idle speed to be certain it's properly set. Also double check both the idle and WOT switches are properly adjusted.

You also should invest in a decent WBO2 gauge so you can properly set your mixture.

If indeed the WOT switch was ALWAYS closed this means that at idle stop both the idle and the wot switches would be closed! If this occurs the DME enters into base idle speed calibration mode, a special mode that only normally possible for calibrating base idle speed. Both switches normally can NEVER be closed at the same time, except when you do base idle speed calibration.
in this calibration mode the ICV is parked at about 10% open and the idle speed control is turned completely off. This explains all the stalling and issues you had at idle.

Yes, as also posted in #103;