It's strange that you have those problrms. I just bought a Nova to use as a second shotgun with a bunch of extra Carlson's chokes and they fit fine. Be sure you got the right Benelli chokes, because if it remember correctly, the crio chokes that fit the SBE don't fit in the Nova. If the chokes you bought were correct, I'd contact Benelli for a solution.
Also, the spacer should have been inside the bracket mount, assuming you bought a new, factory-sealed mounting bracket. Use a piece of thick-walled garden hose, or go to the auto parts store and get a section of hose to make your own.
Overall, I'd say the Nova is a pretty good all around pump shotgun for the money, I'm happy with mine.