I have spent many an hour comtemplating this switch. I have a 2000 rm 125 that uses the same plastic as the 250. I have even gone as far as to buy some used 2001-2006 plastic. As far as I have been able to figure out I think it will work. First, you will definitely need the newer gas tank. Second, you will need the newer seat because the geometry of the gas tank is much different. The newer seat is very flat, meaning that it does not have the arch at the front that the older models have. The panels can be easily made to fit. I have done this myself and it works. The airbox has two layers of plastic, an outside, and an inside. Be sure to only cut the outside. Put the rear fender on first which is a little different as well and the put the panels on. For me, the panels also required that I use a small piece of metal with two holes to move the bottom bolt back about an inch. After that, you are on your own. I have yet to put the tank and seat combo on and see if that works. I am actually a little concerned that "arch", or lack there of, of the seat will cause a problem. If that is the case than I may try and 01' subframe and airbox. I know all of this sounds nuts but its been kinda fun in a weird way. By the way, let me know what you end up doing.
Lot of luck,
Michael Averett