According to my Factory Service Manual for 2nd Gen 600 (GSF600/GSF600S) from model Y(2000) through K3 (2003) all use the Keihin CVR32SS and look the same as your picture...so
A) pilot jet
B) Starter (enricher) jet
C) Pilot screw
D) pilot air jet
E) main air jet
The jet at the 2 O'clock position from a) is the main jet.
You would not normally change D) or E) as they can be adjusted elsewhere and are pressed in, and on your carbs B) looks fixed as well, and would also not normally need to be changed.
As for your jetting changes, I would start by turning out the c) pilot air screw. Carefully turn the screw IN (clockwise) and count the turns they are now, and write it down for further reference so you can go back to stock if needed. The pilot jet(fuel)and the pilot air jet(air) basically control what is a rich mixture that is injected into the airstream downstream of the throttle butterflies. Turning the screw IN reduces fuel flow and makes the bike leaner, turning it out (counter-clockwise) makes it richer, as this screw is controlling the rich fuel/air flow in these Keihin carbs. Depending on what the factory setting is, I would start with 1/2 to 1 full turn out (richer) than stock, or somewhere between 2-1/2 and 3-1/2 turns out from seated. If you need to be over 3-1/2 turns, you should consider a 1 size richer pilot jet instead (A). The Pilot jet and Pilot screw have the biggest effect between 0-1/8 throttle, but do have a small effect at all throttle openings.
2nd, you can consider "shimming" the existing needles in the carb slides. Some commercial jet kits come with needle shims, or you can try and source them from a local electronics supply house or similar. You are looking for small dia washers, approx 0.5 mm thick, that will just fit between the clips that hold the needles and the slide that they seat in, in effect "raising" the needles. For your stock pipe, and/or to start with your modified pipe, use one washer at a time. On my 600, anything over two shims would not fit without some mods to the seating arrangements. I have 1 shim in mine now, but it would be too lean at sea level.
3rd, as you mentioned, you would need to go up at least one main jet size for your modified pipe.
Try to only make one change at at time and see if everything is working. This means you may need to have the carbs off a few times to make the changes as you go. The other option is to look for a commercial jet kit, which may have some other instructions
Let us know how you make out...
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