Stock bore for a while? Here are the XR250R basics.
Pull the snorkel. Replace filter basket with a UNI plastic model, or cut the wire mesh out of the stocker (lots of opinions yes/no on this mod).
Replace the baffle with a '98 and later XR400 baffle. Don't run without a baffle in the stock can - way to loud and hurts bottom end throttle response. You'll have to waller out the mounting holes in the baffle a bit but it will fit.
Pull the head pipe off and grind out the welds that hold the flanges on. There is an XR400 article on Thumpertalk I think with pics about how to do this.
Consider going up a size or two on the main jet after the intake and exhaust mods are made if you get lean symptoms - pinging, running hot, long choke time to keep it running when starting cold, too white a plug reading.
Replace the fork springs with Racetech k430 springs. Replace the stock fork oil while at it and put in 570cc of oil per leg.
Replace the bars with CR Hi Bend Renthals (89-91 Honda CR bend).
Get someone who knows what they are doing help you with rear sag setting after the fork work is done. The short wheelbase 250 is very sensitive to sag settings. Also help with setting up the controls - bar angle, level placement, shifter and brake pedal placement. These bikes can have perfect ergos and really be good mounts for fast/precise riding. Not a girlie bike - a very capable bike that can teach you bunches about corner entry speed, correct use of brakes, throttle, etc.
Later mods: Go to the Wiseco 12:1 5mm over piston. While the head is off go ahead a pop for 1 to 1.5 hours of porting clean up. Just did this on mine (was 4mm over and stock compression). Runs AWESOME. Lots more bottom and mid, then pulls right up to the top. More power everywhere. Should stay reliable, considering at 12:1 and me at altitude it is not even making stock compression at sea level.
Change out and bleed the brake fluid at least twice a year. Like most hondas, the little xr has excellent binders.
Put a Scotts dampner on it when changing out the bars. The bike needs it with the short wheelbase.
Run a 100/100 rear tire, not a bigger tire. Effects the gear ratios and makes it harder to turn.
Buy a case of Castrol GTX 10-40 for cooler months/climates or 20-50 for warmer months/climates and a half dozen oil filters from Honda. Keep the oil fresh in this thing. Get good at filling it up. About 1.25 quarts, then start and run for a few minutes, then dump in the remaining. The oil level is flaky on the bike. Change it often and fill the correct amount, and what the dipstick is telling you is irrelevant as long as it is not burning a bunch of oil.
Have fun with your new mount! Just spent 2 days in Moab on mine. Rode some gnarly stuff (Moab Rim Trail, Porcupine Rim, Hell's Revenge; 5MOH has still snowed in) on the trusty 284 and would not have preferred any other bike.
Leo in Colorado.