1999 cr125r Misses and lacks power?

My 99 CR125 is for some reason missing in 1st and 2nd gear. It is not giving as much power as it can.. Revs fine but just lacks the power. I've rebuilt everything bottom end, top, went thru with a fine tooth comb. For some reason in first and second it misses terribly when I get into higher rpm. Get it in 3rd gear and it kicks down!! can't hold on to it then. Has anyone else had a problem like this and what did you do to fix it?? Compression is top notch. I've not messed with the fuel air mix?? I'm not catching something simple??

99 cr misses

I can't for the life of me figure it out either? The trans is great. I think I'm either not getting enough Air or enough fuel or vice versa?? It just changed after the overhaul.? I think maybe it is an issue with Jetting something I know nothing about. This one is going to a tech who deals with this daily and on dirtbikes. Power on take of is good but when getting to higher rpm it just doesn't have it. I'm sure that others have ran into this and when it gets figured out I will let everyone know what the fix was.