Brad I have an 04 KX500 and have the IMS 3.6 tank, it fits perfectly to the bike. I also have the FMS Gnarly pipe and it clears the tank with no problems.
However the Gnarly pipe did not fit my bike very well. I ended up milling the gasket surface on an angle, bending the mounting tabs and shimming all the mounts. After a couple of hours of fitting , it now fits perfectly. I have three seasons on the tank and one season on the pipe with no problems.
John