You don't run it any different than the 2-strokes mechanically on the dyno, but you'll have to keep in mind that the dyno rpm is going to be lower than the actual engine rpm and the observed torque will be higher due to the gear reduction when you are running it and printing off your data.
Unless you change the rpm and torque formulas in the data aq software...
But even if you don't... because of the gear reduction, the torque difference will calculate out to the same HP end result anyhow with the rpm difference (ratio's), and that is all your concerned with anyhow. Horsepower.
So you can change the dyno data aquisition formula to compensate for the RPM reduction / torque ratio increase or leave it alone and remind yourself about the rpm difference and higher torque observed, your HP numbers will be exactly the same either way.
Sounds like BS, but it is not. Leave it alone and your rpm's are lower but torque is higher = same hp as the higher rpm with lower torque if you change the rpm and torque formula...
DynoTechResearch.com will have your dyno data you're looking for...