Here's a tip for next time.
Whenever I remove one or both of the case covers, I trace out the shape of the case with a marker on cardboard. I note where each bolt is located. Punch a hole and insert each bolt as I remove it.
If you have a fresh gasket to install, you could always trace the gasket.
Also, you learned the hard way why you don't use a drift on the water pump seals. Continue with the socket theme, but fashion one that "pulls". Use a series of sockets and some threaded rod or a bolt. You can press that seal right out with no issues. Check out the MarkNet KLR site for a pictorial