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Not sure if this applies to you but my "99'er had a similar problem when I first bought it. Only in my case the clutch would hang up between gears. As it turned out my problem was due to bad oil in the engine/trans/clutch. Apparently the clutch plates were not releasing properly. Not sure what oil the PO used in the bike nor how long it had been in there. Took two changes before the problem was completely gone. Now it is smooth as silk.
It would seem to me that it would do it in all gears, not just second gear and first gear, like yesterday. Another strange thing yeterday; the cooling fan ran a lot. Was only about 75F, and this is the first time it did that, too. The fan virtually never runs. And the coolant level was good. Poor old girl having a few aging pains I gues. 
Inside the clutch reservoir there is a tiny return hole. If that is plugged by dirt or something, it could cause that. A pin will clean it out nicely.
Of course, if you lived further south, it wouldn't be so long between riding seasons and the dirt might not have a chance to get in there! 
So today I go for an hour and a half ride, got back to town, stopped for coffee, half hour later got on, fired up, kicked her down into first, let the clutch out, nothing. Hmm. Still in neutral. Down into first again, let the clutch out, 50 feet later pulled the clutch back in to roll between 2 parked vehicles, let the clutch out, and nothing, in neutral again. ?? So, kick it down into first again, out onto the road, shift to second, it shifted in to second like a Harley; calunk! ?? Never did that before. Shifted up through the gears, ok, all worked good. Back down to first, took off, into second, calunk! again. Rest of the gears, up and down, no problem. Just going into second from first. Any ideas, anybody? Only around 12000 miles on her, 2002 model year.
Thanks in advance;
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