Did you do anything with the flywheel when you did the clutch? Did you get it resurfaced or did you replace it? Or did you just leave it in the car and just do a new clutch set?

If you are still running stock ecu programming, you should take a look at your mass air flow sensor. It could be failing intermittently. It can fail electronically, which means it would need to be replaced. Or you can remove it and make sure the sensor itself is nice and clean and if not then...