I read this in Rick Sieman's "Tips and Tricks for your Honda 125 Elsinore":
"When installing new main seals, you must slip the crank into the seal at least five times, regreasing it each time. Otherwise, the odds are you’ll pinch the seal when installing the crank. If you don’t do this, the motor will only run five minutes hard before it blows."
Here's the complete article:
http://articles.superhunky.com/4/37I didn't realize the right main bearing had a cover. Maybe it's to keep the seal away from the inner bearing race? If so, I'm real glad it's there. My MR uses the same bearing, and at one point the ignition started double-sparking and created explosions in the crankcase. The left seal blew out, but the right-hand one survived and is still working fine, maybe because of that cap leaving it with no place to go.
I'd leave it in place, I think. Without it, it might be pretty easy to drive the seal in too far and contact the bearing.
Ray