The blow off valve should be set so it blows off well at idle using the soft spring. It will slam shut under load. I have never had this cause a stutter closed or open. If you disconnect the iap sensor and re cal the mapping I bet it will be gone. It sounds like the iap sensor not liking it.
How did you connect the ISC hose .. maby is there the problem .. my GEN 2 is running now good, sometimes the Blow off is stuck ( often when the Bike is without running a few days ) and does not open in idle - but I have no stuttering or so..