Issues getting into second (while moving)

TexasKZ, yea there are differences on the sides between the 2nd/4th fork and the 1st/3rd fork. The big difference is on the side oppose of the neutral switch show in the picture below. Not sure if the picture does a good job of capturing it or not, but the 2nd/4th fork sides are pretty much flat to the touch. The forks are still within the 4.7mm spec and measure almost equally, but maybe its still an issue with one side of the 2nd/4th fork being almost completely flat. 

Have you looked in the FSM for the process for checking spacing and clearances in the transamination?  I haven't done it before, but I think there are shims that you can swap to adjust the spacing.  Maybe it's possible that could help?  Or make up for some wear on the fork?

What I meant was the wear patterns look different on the two legs of the same fork..

Yes, the wear patterns also do not look even on the 2nd/4th fork. I have all my parts coming in by 5/3. I will post back to this thread after putting it back together along with installing new forks, clutch plates, and removal of neutral ball bearings and let everyone know how it went. Thank you all for your help.

With the crankcase just put together, no bolts etc, check the gears and that neutral finder, spin the output/input shafts and see if it selects 2nd those ball bearings may be needed. then just the input shaft and repeat.

good luck

I'd pull the  shaft, roll it on a flat surface to see if it's bent.. I'd also keep the bearings. They're there for a reason.
Steve

Will check the shaft. I cannot see how removing the bearings would have any effect on the motorcycle other than removing the neutral finder feature. I will be test my theory and report back.

Figured I’d make a post now that the bike is back together and has about 75 new miles on it since my last post.  

-The bike runs great for the first time in many years 
-New shift forks have fixed the problem I suppose. I say suppose because on top of forks I replaced the clutch plates and removed the neutral finder bearings. 
-removal of neutral finder bearings seems to have no negative effect on the motorcycle. I greatly enjoy not having that feature anymore

Thank you to all that helped me in this thread.