Hangtime,
I'm assuming you got the cr500 pipe for free, but it might be less work to start with an aftermarket KX500 pipe, specially if you can find one that is built out of cones and not a few stamped shapes like the gnarly. With the different stroke, the CR500 pipe will automatically have the wrong tuned length, but if the rest of the pipe is close, it can be changed by adding a section in the middle. For the headpipe, the critical dimensions are the taper of the headpipe and the total length from the inlet to the midpoint where it meets the fattest part of the pipe. As long as the tapers are close the pipe will work well. I built pipes for my roadracer out of parts of different pipes that were close. I left the headpipe and end cone tapers alone (they were close but not exact), just changed their angles, and tuned the length. It worked quite well. Somewhere on the site, Demographic ( I think) posted a .pdf of the "David Jenning, 2-stroke tuners handbook". It is a bit dated but the formulas for pipe work are very good. Should give you enough info for modifying the pipe. It might be useful to measure the entire stock pipe (or a gnarly) and map it out to scale on paper, ie measure the entire pipe OD at 2" intervals using the centerline of the pipe for the length. Then at least you will have some dimentions to refer to. It's doubtful but if you end up with a pipe that is going to be too long, a cool trick is to cut the stinger where it attaches to the pipe and then slide the stinger inside the pipe and weld it up. Makes no difference to the performance, and makes it quieter to boot. I did that on my roadracer with excellent results. If you can't find the .pdf then PM me and I can email it to you (it's on my work computer). Also consider looking at the zip ty pipe as it has a unique shape to clear the tank that could prove helpful. Here is a pic of the zip ty. For pipe work a power hacksaw or bandsaw is very handy. Makes it easy to slice a small 1/2 pie section out (to weld on the other side) to change pipe directions. Have fun. Cam.