I'm leaning tward the mainshaft gears. Because the shift rods and forks are not adjustable, 3rd gear may not forward (deep) enough into the first motion shaft.
Do you know the correct method for installation of the rear mainshaft bearing. when I first installed it, I pressed it all the way down to the shart sholder. After installation of the mainshaft I noticed the the mainshaft and layshaft gears did not line up. I took out the mainshaft the brought the bearing up reinstalled the mainshaft and tightened down the end nut until the gears lined up.
This may be my problem, how do I measure the correct position of the mainshaft and bearing?