I put everything back together and ran through the gears but it seems like the spring on the front bolt of the pivot cup backs out. It gradually becomes harder to locate the gears. I can pop the spring back in place by pushing on it.

Also the ends of the spring doesn't sit on the rear bolt of pivot cup like in this picture:

 

where did you get it from?

 

Short shifters are going to be harder to push than the stock shifter. Are you sure the short shifter is made for the evo? Recheck your installation and also you might want to check the underhood bushings to make sure there are no problems there.

I messed up that spring on the side of the shifter when I installed my Works short shifter awhile ago, but after installing it correctly, no problems for over 40K miles.