depending on what your intake/exhaust setup will finally be, you can check the jetting database for good starting places on how to initially set your jetting. after that, it's fine tuning for your location and particular bike.
you can start all over w/ plug checks, but why do that when people before you have done the work, which is sorta the reason for the database.
I mentioned plug checks for Hokie cause I have not seen a stock exhaust used with a pulled airbox configuration before and was giving him a best guess on a main to start out with.