I´m not shure about the measuring method of Dynojet yet. As I know in the past it was always the power at the crankshaft. May be I´ll wrong.....
I haven´t said that you "must not", but you should not play with the pilot screw. You dont need to change the configuration of the pilot screw in first stage, because this influences the idle speed and fuel acceptance at all, and this system uses a completely different system (called slow-system) as the main sytem (it has its own "pilot jet"). DynoJet-Kits are normaly designed for the main-system! I know that there is a new pilot jet in the kit for the GS500F, but I´m not sure if you can use the same screw position for the EU-Version. In the past we never needed to change the position of the screw, even with the new pilot jet..... and if we did it, we had much troubles to find a good ballance...
Let me explain, why I said this: The two pilot-screws are presetted (ballanced between both Carbs and to the main system) useing a highly sensitive measure system (it ballances the production tolerances also). These system influences mainly the range of 0 to about 1500 r/min and fuel acceptance in low range . Normaly, DynojetKits rather have no such a great influence to this low-range, that you have to chance the screw position (we did 5 bikes so, btw, don´t forget to tune up the airbox too.....)
Be carefull, you can cause such effects as "rotation needs a long time to come down to idle speed (even throttle is closed)" and so on....... The hint in the service manual (3 turns back) is only the last rescue and very inexact and is quite different to the DynoJet-manual.....
So, I think, let the screw first untouched, and turn it only when you have problems with idle speed or fuel acceptance in lower range. When you do anything with the screws - do exactly the same to both carburators (and make a notice what you have done).
Hope, I could help to prevent you from the same mistake we did first, and which takes us a long time (and much coffee) to get back a smooth running engine.....