bog at 1/2 to wide open throttle

Don't know if this will help but from a Yamaha parts catalog looks like it came std. with a #45 pilot and a #350 main.

You may want to check the top end. I bought a 1991 RM 250 from a guy who said he rebuilt the top end. It was really hard to start cold, but would start first kick when warm. It wouldn't idle for anything. It also backfired like crazy. Sounded like a gun once in a while. I adjusted the carb and rejetted. I thought the jetting was off because I put a new FMF Fatty pipe, Twin Air Filter, and Boyesen reeds. I tried everything with the carb. I checked the compression and it was low (150 PSI). I pulled the cylinder off and the piston was cracked clear across the top and around both sides of the skirt. I learned the hard way that you can mess with the carb, but with top end damage you'll never get it to right. I can't believe my bike ran at all. If you bought it used it's probably worth a look anyway. I hope this helps and I hope you don't find a wrecked piston and cylinder like I did. At least I found a solution to my problem even though it was expensive.

My MX125 was giving me similar trouble. It would be fine to about 1/2 throttle and then bog and cough. As it turned out, it was too rich on the main and the needle and flooding the bike out. I leaned out the needle and the main, pulled the pipe off (and dumped the gas out of it), and kicked it a million times with the gas off and the plug out to clear it out and now it runs great.