Ok so.
The head is back from the Machine shop. It was still good and is now at 3.521" bore. The #1 got some pretty aggressive cleanup then a hone then a measurement at which point it measured out to 3.5203" , the machine shop brought them all to an even ~3.521". I spoke with the folks at promarineus and they were very helpful. They have done a lot of work on these engines and suggested a clearance of piston to bore of .0004-.0005" based on the pistons being .00035"-00045" under the prescribed bore size of 3.520", I think 3.521" on the money will give the clearance I need to not have a hot("cold") stick happen again. I'll be reassembling the motor on this coming Saturday 07/22 and taking it seriously easy on it for break in.
Additionally the entire exhaust housing is completely torn down and has been gone through to make sure there is nothing to possibly cause any flow obstructions/restrictions. The entire water flow path has checked out. The entire exhaust path has checked out. The plugs are(and have always been) ql77jc4 and are new. The carbs were torn down completely orifices measured, floats needles and seats are pristine, leadshots pried out and replaced. Reeds are all excellent.
Other things being done are drill and tap the tops of each waterjacket and the water chest for 1/8" vent lines to run to a pisser on the SB side just to be totally sure that there is no chance of a possibility of air entrapment in the waterjacket causing boiling. I have the Arduino, K-type thermocouple, 3.5" tft-lcd 4 point temp monitor up and running. It's very crude and pretty slow on screen refreshes. Turns out the best cheapo board to do this with is an arduino Due, it's faster and can keep up with the screen refreshes.
Being that everything (everything) checked out I'm going to have to go with the belief that the #1 cylinder was just enough undersize that it could idle and be run to 4k-4.5k and cool adequately to not seize. My best guess it that even at 4k the piston was dragging a little making excess heat from friction. Take it any faster and the heat goes way up.
