Hmm,,this sounds kinda tricky. But it must be something simple. The are brutally simple machines, they don't run super tight tolerances on these shifter components,but they are accurately built and require a careful eye sometimes.
First things first ,though: Pleeease don't run without a gasket. No gasket=oil leak=slippery back tire=
The first thing that comes to mind is how the shifter shaft mounts in to the case. It just slips in to a bushing in the engine case and the shifter cover supports it with a bushing as well. It possible that the shifter shaft is not fully seated somehow, allowing the shift cover to pinch something.
It may not be the shaft itself, it could be some part of the linkage itself.
The stud that all the shifter parts mounts to (with the multiple washers/springs) may have something out of order causing it to bind on the cover somehow,but I really don't recall those part running close enough to the cover to do that. The tip of the stud that the nut goes on protrudes the furthest of anything, and it obviously clears the cover just fine as it is.
Something has to be hitting the cover and getting pinched. It's the only thing that makes sense.
Are there any scratches or witness marks on the inside of the cover? That should give you a clue.
But please...no silicone...and no running without a gasket.
I'm usually pretty good for throwing caution to the wind, but these are two things I wouldn't dare do in this situation.
Good luck fellas. Keep us posted on what you find,please.