Depending on miles on the sled I would change the reeds (V-force-Boysen-or just replace the petals on the stock ones) and do some clutch work. Try something around 51g weights, the next size up on the primary spring (should be orange/white unless you choose another brand) and a different helix.If money isn't that much of a issue, buy a complete clutch kit and chip it. You could just try the heavier weights with a new primary spring (yellow/white) as well, might be your best bet. I wouldn't bother with pipes and stuff like that.
D&D and Black Magic both make chips for that model sled.
Just about any company out there makes a clutch kit for that sled. I have specs on a 00 ZR600efi but it is slightly different than yours. The helix was 56-44, 53 gram weights, oem orange/white primary, and stock secondary. The helix should work ok, better if it was chipped, the 53's might be a little to heavy for that sled (which is why I recommened the 51's). My buddy did the 50.5's with only new oem springs and made a big difference (he has the same sled as you). Make sure all your idle wheels, bearings, rotating parts (don't forget clutches) are in good condition as they cause drag and rob alot of HP to the track.
Bottom line....the only things I would do to that sled is 96-144 picks (depending on riding style), aftermarket reeds, clutch work (mainly what's mentioned above), efi chip.