I would take the box out myself, just to be sure, if the seal can be replaced with box in place thats fine but at least with the box out you can make sure its sitting correctly, and there is no damage to cases and shaft! I dont know if there is any damage, but something isnt right, I didnt replace my seals, but i made sure they were seated correctly and the spring was sitting correctly, i also checked the bearing and shaft for damage. Mine dosent leak so something isnt right, so wip the box out and have a look, Its very very easy! the hardest bit about the whole job is getting the engine case back on, and craking the clutch nut!!! the box slides out after you take the 8 bolts out!.

Just had a thought!!! is there any play back n forth in the shaft? (back to front as you sit on the bike?