I modified my stock muffler by cutting the end cap off and removing thye baffles. I now have a 1 1/8 in. pipe coming out of the end cap. I need to know how to jet the bike now so I wont hurt the engine and so I can get the best performance. Any help would be great. Thanks.

P.S. It has a Keihin carb.

 

Is it a stock carb?
If so I would replace the needle as well. Don't forget to drill out the slide valve with 7/64 bit and drill out the cap for the airmix screw. Turn the screw out 2.5 turns (the non-centered hole).
With that big ol' butt plug muffler end remove I would go with either a 128 or 132 main. Assuming you are 3K and below in elevation.
I did the dynojet kit without any muffler mod, I am using a 124 main. runs PERFECT.

I saw this in another post:
KLX300 parts to replace in the KLX250 carb:
# 16009-1912--------Needle-Jet,N1TC
# 92143-1667--------Needle Collar (required for N1TC needle)
# 92037-1401--------Clamp, Needle Jet (Clip, required for N1TC needle)
# 92063-1069--------#125 Main Jet
# 92063-1074--------#128 Main Jet

what I used:
----# 2206--------------DynoJet Kit