KTM 350 bench shift issue after rebuild

I rebuilt mine last year and neglected to bench shift.  Got it all together only to realize it wouldn’t shift at all. Took it apart and I had misaligned the shift fork in the round thing with grooves. Adjusted it and it fixed it. I would check to make sure forks are aligned in the correct grooves. Here’s some pictures

A transmission will only fit one way allowing the case halves to contact. Did you oil all the parts before install?, there is a great deal of friction in there.

What year is the bike?

I'm having a similar issue with Husqvarna TC85, bike had been run with no air filter and sucked what can only be described as a swamp into the engine. All gearbox bearings changed, crank, big and little end bearings, new conrod and piston. Tearing my hair out trying to workout why the gear selection is so problematic. Never had this issue with a rebuild before.

Are you sure all rhe bearings are seated?   Are shift forks in right order?

I went through all the gearbox bearings last night, made sure they were all seated correctly and more importantly made sure they were all the correct width/depth, according to the parts books the correct sizes are installed. I put the crank cases together with the individual shafts installed on their own, neither show signs of tightness when not in together. Would it be possible for someone to send me the workshop manual pages relating to the gearbox installation? I can then go through exactly what is recommended correctly and hope I can see what I'm getting wrong. I've had many of these things apart over the years and this is the first time I've encountered this. 

Sorry to the OP for hijacking the thread, but I can see it being relative to my issue too.

Not a silver bullet, but you can find free manuals here: Free Manuals 1994 – 2014 – Kristofsx.com | KTM Repair Manuals

The KTM group bikes haven't changed much from year to year and you can likely find a useful starting point for orientation of things.

@Mucktub @wiggins419