After numerous dyno runs, drilling jets etc over 10 years ago I no longer have the specifics of what we came up with and also there are no jet sizes to go by as we used drills. The tuning was made to suit an engine with open airbox using a modified K&N insert, ported and flowbenched head, high lift cam, 672cc high comp piston, removed rev-limiter on a stock CDI and a fully open exhaust.
No change of pilot jet as I recall though. I dont think Keihin jets fit, haven tried it so I can be mistaken.
I have read that Egli recommends to go down from a #140 main jet to #102,5 in the left carb and up from #165 to #175 in the CV half for stock engines, mixture 2,5 turns out, needle position according to what works best for your bike. This is for stock engines with K&N type filer, slip-on and a Tunebike venturi mod. The above mentioned Jet sizes should be avaliable from your Yamaha dealer.
Klicking:
viewtopic.php?f=3&t=1157& will give you specific info in the various stock jet sizes for diffrent incarnations of the 660cc 5-valve engine.
If you are having problems with the set up make sure that you cleaned the carb thoroughly including the little mesh filter in the carb housing on top of the float valve AND check that the diphragm in the CV carb is seated properly.