Just as an example, this pipe should work:
http://cgi.ebay.com/ebaymotors/NOS-Hond ... ccessoriesThere's also the Bassani MT250 up pipe, which was offered as a factory option at one point. They come up on eBay fairly regularly.
The MR250 pipe is made to fit the later 250 cylinders, with the exhaust manifold on the left side. It would take a whole lot of work to fit one on an MT.
Your stock pipe is probably clogged with carbon (NOT in the removeable baffle, but in the spark arrestor where the tail section meets the main pipe body). Drilling this out with a 1/2" or 5/8" drill will make a big difference in mid and top end.
There's quite a few differences between the MT250 and CR250 frames, if you look closely - more than just brackets and mounts. Just two nearly invisible mods - changed steering tube angle and footpeg placement - can make for an entirely different-handling bike.
Ray