Was there any grooving on the sidewalls of the shift drum slots?
Guy from what I've been told there is one small spot on the drum where there looks to be a little ware.
Check all the mating surfaces width, the groove on the barrel, the pin and tangs on the forks, the groove the fork rides in. all the clearances are cumulative. Also roll the slide shafts on a glass plate and check the gears for rocking on the shafts, any combination of these together can cause the issues your seeing for the neutral trouble.
Do you know what the specs are for the pin, the drum grove, the tangs, and the gear groves?Were the forks replaced with the backcut, they usally need to be if theres any jumping out of gear . They get tweaked by a few thousandths and it's not noticable unless installed and moved just rite.
I do not believe the forks have been replaced, so just a few thousandths will cause it to slip out of gear even through their back cut?
On a side note my trans when it was back cut has machining on the forks but since I bought the motor with the work done I am not 100% on what they did to the forks.
Thanks for the help