This question is on my son's thumper, but this is something that's not 2 or 4 stroke related, it could be on any bike.
I finished rebuilding my son's 06 KTM 250SXF..  when we got the bike the engine was disassembled and in a crate.  We put in a new crank, bearings, piston, rings, etc.  Basically a two stroke bottom and top end rebuild, as the valves were all in spec...  (Thank God)...  The bike runs well, (for a 250F), but I'm having one issue...  It's really difficult to find neutral.  When I do find neutral it seems to be between 2nd and 3rd gear...  but to find 1st gear, it only takes on click down...  My only thought is I have something wrong with the gear selector.
From my manual here us the installation of the gear selector.  

It really only goes together one way, and I believe I put it together correctly, but...  something is not right.  When I had the cases open, I left the tranny in the side case, and never pulled it out.  So I'm leaning towards the gear selector.  
Any thoughts guys.