Remove the shift tower,first making sure the shift lever is in neutral and the reverse lockout shift latch is facing down.
If the 3 shift forks are in the proper neutral position,move the 1 & 2nd and 3rd and top sliding gears to the neutral position,using the forks as a guide,then drop the shift tower down(make sure the gasket is in place first),and you should be right to go.
If you''re still having problems,check to see if the shift fork rails have been moved out of their proper positions,because if they've been moved,the shift pattern will never be correct.