Re: vapor lock
And you've checked the fuel pressure while the problem is occurring? If not, I still vote fuel pump - they'll work great once they cool down but when warm they'll "fail." I believe the pump gets so hot it'll vaporize fuel as it passes thru; technically EFI is not supposed to vapor lock like a carb, but I believe this is a form of EFI vapor lock "so to speak." The problem is exaggerated as the fuel level in the tank gets low, the pump is immersed in less fuel and also runs hotter as a result.
Healthy pumps will not exhibit these symptoms but IME this is how many of them start to let you know they're tired.