Has there been any maintenance into the underbelly? Has anyone messed with the tranny? bottom side rebuild? I found my post from last year, (it was on the bottom of the page)
http://www.xs400.com/forum/showthread.php?t=8112
you can see the tranny there, and you can see how difficult it can be to get everything put back together. Perhaps one or more of the forks got bent, perhaps the installer couldn't remember what grove to put the forks guides into the right pathways. I know I was concerned on that cause the guides would get locked up, till I got the rest of the transmission into it.
There was also that big oddly shape shift lug? that had a spring loaded pressure thing going on, it took me a couple trys to get that right too.
Clutch lever,(cable) there is a procedure in the manual that says to lubricate it, I didn't do that, but i did have to tweak the Clutch rod spring. Mine a little dab of JB weld, fix. The spring hole, had started to wear a hole all the way to the outside. that dab of jb weld reinforced the spot. so perhaps that clutch rod assemble might need some grease/TLC.
FYI-- I figured out when I was testing the gears, with the bike off, and up on the center stand, I could spin the back tire, and then I could shift though all the gears, up and down. That was my warm fuzzy feelings that I got it right.