I was having this issue and it turned out to be the throttle body. Like you I reset to stock with the stock TB and then it was fine for awhile. The issue kept happening so Edelbrock replaced the TB and I havent had an issue ever since.Update #2: I was having significant issues with the tune. Flat spots with virtually no throttle response during random cruising and also when coming out of boost. Then it went in limp mode out of nowhere and CEL came on. I pulled three codes all related to PCM inputs- throttle position, IAT sensor, and ABS.
I decided to revert the tune back to stock and then re-program the car with the EB tune. So far, driveability has improved drastically now that the TB is operating properly. There is still somewhat of an on/off switch, but much better than before.
Still may go the custom tune route and I have OPG/CS on order.