Unfortunately all you can do to check the bottom end is to spin the crank by hand and listen/feel for binding and roughness and checking side to side play.
Excessive side to side play can let the rod tilt. Measure it and compare it to the spec in your manual. If its close to max replace the crank and both side bearings. It is a very important measurement. Of course ANY up/down play and it needs replaced ASAP.
Also you can look around the clutch basket, kick starter gear area for anything that would bind up, but that's all you can do.
After that you have to replace the crank and bearings. Also wise to replace all the transmission bearings too while your in there
When you say spin by hand, using a socket on the crank case side? or grab the piston rod and move it through the motion?
I took the trans case cover off, nothing appears to be broken/chipped, warped in there. The only thing that looked weird to me was the spring for the kick lever, but I'm not sure how that normally looks to compare it. (edit: looking at photos of a kick starter spring and sprocket online, my spring is clearly bent out of shape. So I will order a new one, but I don't think this is what caused it to bind.)
This is my first time working on a dirt bike motor, I'm a car guy.
Edited by fldrifter, December 17, 2013 - 11:21 AM.