Are you running the correct map for stage 2 and the intake you have? What TBE do you have? Have you cleaned your MAF? Are you using the airbox with that intake or are you running the hot air version? So just to clarify, you've always had this issue, even before going stage 2?
The behavior you're describing isn't really abnormal for a manual car. Often the RPM will drop below the normal idle level after you rev it because of the loss in engine momentum causing it to drop, and the car taking a second to recognize this and correct it.