With my LT I was at this point. I just went in and re did the bottom end. You already have the motor out and the top end off. You might as well take the extra bolts out and split your cases to check for additional damage. It is the only way to know for sure. When I split mine it was my first time but with help from the forum, and those manuals that I posted you should be able to take care of it easily.

I thought that for me at least I would hate to put money into re doing the top end, take it for a ride then have something drastically go wrong with the bottom end, which would cause you to have to purchase whole new cases. when you could of spent the extra $200 and extra week and it could have been prevented. Either way we're here to help.