I agree with GT, leave the flappers be. Not gonna gain anything, and if you do mostly river running, even more so as currents can easily waterlock the engine depending on which direction you're running and lift. (see the same thing on the lakes here at times, when they open the locks the current can be extreme at say Saguaro or Canyon lake).
You also need (required) a USCG Flame arrestor in all 50 states on all boats, from what I've found out. I would look at ways to direct what airflow you do have to the engine as it is maybe a bigger flame arrestor, again, as GT said. (Which, to my mind, is that not what a cold air intake does anyway?)
While we're on the subject, when did the BS Honda guys start making "Cold Air Intakes" for watercraft? Missed that evolution.
If you want more performance from the exhaust, gonna hafta go with center risers, TT or OT headers. Pretty much you're only options.
Again, just my .02
Ray