So, are you using the stock air box as a manifold that a K&N filter is hooked up to? Give us some specs?
I've always found that a Honda just runs better with a stock air box. Rather than run a stock air filter, the K&N was modified to be on the outside. The rest of the engine other than removing the starter and alternator and the Kerker exhaust is stone stock. Lots of one-off pieces, hand made rear sets, clip ons, brake control rod, muffler hanger, engine covers, fairing and tach mounts, a widened Yamaha front fender mounted backwards for the rear subfender, vented rear hub, dual disks with the calipers at the rear, laid down Boge Mulholland shocks, progressive springs in the forks, a hand made fork brace and a few other tid bits here and there. A lot of the aluminum machine work was done by the gentleman I bought it from. He was an artist with a lathe and a milling machine. I fabbed the tail from scratch in fiberglass, made the seat, and painted everything. I got this as a rolling chassis, and it only has about 20K on it. Runs and handles great.