Hey calm the ego Mr. "I can trouble shoot everything". if you REALLY think you are so great we might have a project at our shop that you should come look at. Besides if you are SO good why do you need us? you would have thought of everything already...
Anyway...here is some help although i'm sure you dont need it
coolant temp sensor problem?
Coolant problem (getting to hot after shut off due to air in system and heat soak) thus causing high Coolant temp readings and weird start up
Intake air leak somewhere ...only evident when hot and things have expanded and opened up a bit.
Vapor lock in fuel rail, due to too much heat in fuel rail....no phenolic spacers?
is the EECS COMPLETELY stock?? if not it could be a weird relationship between what ever parts are not stock. i.e ecu program, MAFS, injectors