does the kit instruct you to drill out your slides then plug them? If so, it's basically a Dynojet kit. Although at least is sounds like they are still using mikuki jet sizes for the mains.
You say your bike is still stock with airbox etc? try using their 125 mains, keep your original jet needles, but put one #4 washer under them, chenge out your pilot jets to 40's instead of the stock 37.5's, then drill out the caps over the air mix screws if they haven't been already, turn them all the way in (clockways) and then back them 3 turns out. same as you have written above.
OK put the factory needle and your stock needle side by side ... do they look and feel identical ... if so you are fine ... swap to 40 pilots and do theyr needle in the position that will be 1mm higher than the stock position and 125 for a stock bike, and 127.5 for a K&N in air box. Leave floats at stock height ... if the needles are waaaay off .... OK I have no idea ...
Cool.
Srinath.
For the record, Factory Pro Kit's do not require any drilling.
Oh...and I would recommend their kits or Ivans over dynojet or K&N anyday. Ivans only does a few bikes though. I had really good results with a factory kit and ign. advance rotor on my ZX6E. It was like a different bike.
However for the GS I think the best route is just to buy the jets and follow srinath's recommendations. Save alot of $$ doing it that way. I'm gonna rejet my SV that way to after I get a slipon/desnorkle/tank spacers.