Dynojet makes the power commander, not FMF.
FMF does have their own programmer.
So we need to know which one you have to help out.
If you have an actual power commander you just need to load the appropriate map for it using a USB cable and a computer.
For the FMF programmer you just have to manually make adjustments. Either + or - on fuel.
Looking at your mods, you do not list an actual intake, just K&N. Do you have the K&N intake or just a K&N filter on the stock intake?
99 Honda 416EX - Basically Everything
08 KFX450R - Pro Circuit TI-4 Full system, KN intake, PCV, Hotcams Stg 2
99 Z28 M6 - H/C/I/N2O - 26MPG - NA 430rwhp/403rwtq 12.8@115 / 150 shot 591rwhp/649rwtq 11.4@129
09 Yamaha WR250R - Street legal dirt bike - 65mpgs of awesomeness - Stock .. for now
93 Eagle Talon TSI AWD 5spd
Evo3 16, 272 cams, Evo 8 Rods/Pistons, 560cc injectors, 2G MAF, DSMLink @ 17 PSI