UPDATE:
Took the bike into the dealer today to see if they could figure it out.
Before heading there I put a couple of thicknesses of electricians tape between the throttle arm and the stop screw, so as to effectively open it up a slight amount when "closed". Guess what? When I got there it was idling fine.!
They ran diagnostics and said everything checked out. TPS, IAC, MAP, injectors, all good. No cracked or broken butterfly shaft.
In short they could not figure out why it had been stalling, and they could not duplicate it with the throttle against the stop screw the way it should be (ie tape pieces removed).
What they did find is that it has a 103" race tuner download in it, apparently installed by the previous owner. Considering this they suggested that I disconnect the PC III tuner (overkill) and try that out. Guess I will do that and see what happens.
I did not get a race tuner with the bike, so I guess this means there is a loose race tuner sitting in someone's shop drawer somewhere, which is totally useless to them, since it is married to my VIN.
The weird thing is this flash was installed before I got the bike, back when it was a stock 96"!
The dealer folks were really nice, and the tech seems to know his stuff. Been working on Harleys for 20+ years. Its really nice to get to talk to the tech, and to even get to go into the shop and see exactly what he sees on the digital technician screen. Most dealers will not let you do that at all. Love it. And the service manager is a really knowledgeable long time Harley guy as well. Very helpful dudes.
So the jury is out as to whether it is fixed or not. Ran fine on the way home, and idled just fine when I put her away.
Who knows what's next?