2007 ninja 250 can't get out of neutral

[LarDog]

I have a 2007 Ninja 250.  The engine had a bad crank and cases.  I got a 2001 crank and cases from Craigslist.  I got rid of my crank and cases and put all the parts and pieces in the 2001 case.  The engine runs (see my carb vacuum hoses post), but I can't shift the transmission out of neutral.  It will clunk sometimes and the neutral light goes out but it is still in neutral.  I've tried putting it in 1st and 2nd but nothing.  I've tried all this with the bike on the center stand.  I'm going to try taking the shift linkage off and try to put it in gear with another gear shifter I have lying around.  The thought is maybe the linkage needs to be adjusted.  I have not messed with transmissions before and I'm at a loss of what to do or try.

 

Thanks for any and all help