I don't know much about what happens to the seal with an overfilled transmission, but one thing I do know is that if you have a bad transmission input bearing, there will be some play in the transmission input shaft that could also damage the seal. But that play in the input shaft results in an extension of the clutch lever when up-shifting through your gears. When you accelerate, the clutch lever wants to push outward because the transmission shaft is actually moving.
Very bad news, because a transmission rebuild is the only play at that point. When you had it torn down to the inner primary to change the seal, was the input shaft really solid? I'd think that would be harder to detect with the primary chain and clutch all in place....the only movement should be rotation...if the shaft has any play at all, that's a problem.