How to restore Louisville Slugger 125 bat with 2 bad water damage to the end near Yogi Berra emblem?

Usually water damage cannot be repaired because it goes past the surface and into the wood. There is not much you can do. As for cleaning the surface of the bat you can use Formby's furniture refinisher to clean any residue, or paint, and you can use a 0000 steel wool pad. When clean and dry, use Min-Wax paste wax and buff for a nice Finnish.