You haven't said who's NOS stacks your using. If it is the Honda ones, you want to use two sets of the 2/3 stacks, as the 1/4's are bent to fit the plenum. Then add some foam filter socks (make sure to oil them), and zip tie in place. Doing this won't change the tuned intake track length, and result in jetting problems.
Regarding jetting, I use the following to get close, then fine tune from there.
Exhaust change - up one main jet size. If this isn't needed then that exhaust isn't anymore efficient than the stock, wasted $'s.
Air filter change - up one, possibly two depending on the setup. Putting a K&N in the stock air box would be a one. Anything else is probably going to require more.
Exhaust, and filter change - two sizes for sure, most likely three for the combination. The slow jets may need an increase in size as well.