Hondata

I have a 97 Prelude SH, i have done quite a bit of work to, i am running N/A. I took the car down to get the Hondata P28 w/OBDII adapter on it, installed and tuned. On the first run on the dyno with the new ECU installed, the CEL came on and registered a code 9, CYP sensor. I couldnt do any tuning on it with the cel on. With the stock P5P in it, it doesnt come on. I took it to honda to check it, and every thing tested fine. I have no idea what is going on, and i really need some help. I know that the cyp sensor in the 4th gen prelude's has a different # of teeth on it, i didnt know if that might have something to do with it? I am just trying to find out what might be going on, i really need to get the hondata ECU installed.

Mods.
-AEM Coldair Intake
-AEM Fuel Rail
-AEM Pressure Regulator
-DC Sports Header
-MSD Ignition and Coil
-Unorthodox Racing Power Pulleys
-Clutch Masters 8 lb. Flywheel and Stage 3 Clutch
-Nology Plug Wires
-Denso Iridium Plugs
-Hondata Intake Manifold Gasket
-Powercore Exhaust 2 1/2
-STR 70mm Throttle Body
-EGR Block Off Plate
-High Flow Catalytic Converter
-Skunk2 Cam Gears
-Skunk2 H22 Stage 2 Cams
-Skunk2 Retainers, Valves, and Valve Springs
-Spoon H22 Thin Head gasket
-Port and Polish on the Head and 3 angle valve job
-Port and Polish on the Intake manifold

I figured out what the CEL light was due to. The head has been milled and a Thin headgasket from spoon. These two factors happened to advance the timing on the exhaust cam. The reading the P28 was getting once the car ran up to 3500 RPM, was making it think the CYP wasnt lined up. I retard the timing on the cam, and i dont get the CEL anymore, the problem i have now, is it wants to hesitate (its not leaning out, or getting rich) around 6000 rpm. I am not sure what is causing it. We tried several times on the dyno to get it set, but no luck. I came home and played with it some more. It runs good sometimes, and then others, it just hesitates for a second.?? ANY CLUES, what it might be. I adjusted both the exhaust and intake, almost back to TDC on the cams. For the CEL light to stay off the Exhaust cam just has to be retarded a 1/4 of a degree on the cam, so i dont know why it has that hesitation in it, when the cel comes on the is no hesitation. PLEASE HELP ME!!! It is driving me nuts. Thank you, jason