Here are my mods, what would you add to get the most out of a protune

Currently running Cobb Stg 2 AP (93 base map)
Maddad V2 Catted DP 3"
Ultimate Racing Ti tip exhuast 3"
Perrin Crank Pulley
Drop in K&N with silencer hack

I had a Typhoon intake, but my boost was hitting 19-20, so Cobb told me to go back to stock box.

What other items would you add to get the most of the protune?

If I get an intake again, can the car be tuned to use the intake well, or is it still best to be on stock box?

Opinions and flames welcome.
Thanks guys!

UK