Sounds like the idle is set to low. When you say stock, I'm guessing the tors are still on the carbs. Look at your manual and it will show you how to adjust the idle speed (two big screws on top of the tors) They must be adjusted the same amount. I would also check the air cleaner.
If you have the tors removed and have the aftermarket idle screws on the carbs, turn them all the way in just in till they make contact. turn them out 1 1/2 turns lock the nut down and go from there.
One more thing, with the air cleaner removed look into both carbs and make sure that both slides are moving at the same time (one not befor the other)
Hope this helps