Is there anything that could be done with the stock exhaust system on 98 SPX. Like a better routing or a water Bypass mod?

If I remember right, I screwed my RAVE water injection adjuster (red cap) on the water box all the way in and backed it out 2 turns to help limit the amount of water being injected in my water box to help my bottom end.

Some people took the RAVE adjuster off and screwed in a brass fitting with a 80 or 100 gram main jet.

Yeah what rx951 said, you can jet the water injectors.