On my 04 kx500 the funny noise was caused by the upper pipe mount. This is on the right side of the bike . The frame broke out and at certain RPM the broken mount would vibrate against the frame. When I first heard it I thought the KIPS was rattling. I now have learned whenever I hear a noise like this, it is related to pipe mounting.
I also had issues with springs falling off, when using the stock pipe. With the stock pipe I used shorter springs from an orange bike. With the FMF pipe, the stock springs seem to stay on.
John