I just picked up a very cherry 1996 XR 250 and seek jetting advice. Most of the stock equipment, including jetting, is still in place.
The airbox baffle will be pulled, the stock airfilter replaced by a Twin Air, and an aftermarket insert (Thumper?) will be used.
I'm located less than 1000' above sea level.
With that much more air flow your going to have to probably jet that bike pretty rich. IMHO I think its always better to start too rich and work backwards than viseversa. Get some richer pilot jets and some richer main jets. and have some fun.
I'm at sea level. I went up to a 48 pilot & a 138 main. I got a bit of hesitation but opened the mixture screw about 1 turn and everything works fine. I have a uni filter and hrc baffle from baja designs (kinda loud). A lot more power!!
Your best bet would be to contact XR,s Only. I put a K&N on my wives, Supertrapp, opened up the airbox etc... and the only thing I had to do was go one up on the pilot. I called them and told me without hesitation on what to do. Good people.