Last fall my 2001 YZ250f was being ridden by my older stepson, who goes about 240lbs, in just first and second gear, since it was the first time he had ridden the bike (I just bought it earlier in the year and started riding myself). When he came back with it after about fifteen minutes, the header was glowing red hot, and I thought it was fried. After I got on it and rode it hard for a little while it cooled down, but was still glowing orange. Nothing seemed to be amiss, though, so I didn't worry too much about it. After posting this question over the winter, along with a few others, on this forum, I checked the valve clearance (right on), and flushed the radiator. I also added "water wetter" to the antifreeze/water solution. The bike still runs hot on trails, which involves a lot of slower riding at times, but I haven't seen it glowing red hot again, and the antifreeze isn't boiling over as much. The service tech at the local Yamaha dealer said that it wasn't that unusual for the pipe to get so hot, and he didn't think it was cause for any concern.
One other note, I checked the idle timing, which should be about 1700 rpms when warmed up, and found that it was a little high. I also try not to let it sit and idle for very long, regardless (although it is a pain to restart when its between the cold start and hot start settings - I'll be putting a "hot cam" in it this winter when its down for service!). I hope this info helps.