2008 yz250f freed piston up finally now what coused it? the things that didnt are ...?

i took left side cover off and had spin it backwards to free the piston piston is moving smooth as could be by kicker now no play on left side of flywheel stator side so dont thing crank crank bearing bad could they still be and what are things i can do to check it bike rolls in gear and in neutral. i took head cover off checkd the timing and did valve clearence check both was good so next thing im going to do is take the cylinder jug off and check valves piston crank rod and w/e else timing chain also look good and was tight. so what all could it be i am stuck on valves or valve messd up.so what all do i need look for n check when i tear topend off also what do you think it could be doing to be locking up like it has? thanks !!!!!