I had an old article where if you want a thinner rear section on 1989-2001 CR 500 you can install a complete sub frame airbox SEAT AND FENDER FROM A 1992-1996 cr 250 BUT YOU HAVE TO WELD ONE BOLT TAB ON FRAME FOR SUB ALIGNMENT.
Dirt Rider March '96, the Pro Circuit built CR500 for Rich Taylor. I'm guessing that's the "article" you're mentioning?
The benefits of this are really aesthetic only. Especially for trail riding...you want that soft couch to sit on. But maybe a good face lift for the die hard steely rider?
My 89 has a 91 125 sub and seat, rear fender setup. Everything lined up just fine except the back silencer mount which was about an inch off to the inside. I just run the front for now but do you think the sub frame may be twisted or something? Everything else lines up great.