If you dont have an after market air filter yet, its a worth while investment. Also, if you can find a way to eliminate the stock filter cage/ back fire screen that will help too, Assuming you have the typical honda cage with small holes. Some aftermarket filters come with their own cage. Be ready to re-jet though because stock filters and cages really restrict.
Can you re-route your intake duct to the air box? The original intake tract on my quad was about almost 5 feet long. Hard to believe the motor even ran but it did. I was able to shorten it up to about 1.5 feet long by making a snorkel up to my handle bars and in doing so Gained a little power.
Besides possible hard facing of rockers you may also need to replace valve springs, seats, and valves themselves otherwise they will not hold up. I also heard that hot cam has a cam that works with stock motors.