This is a series of three videos (see link below)that show you how to do a bottom end rebuild. It includes tools needed and inspection tips.Go slow, split the bottom end, replace the gaskets, main bearings and seals as you go along.As I remove each assembly,I place it in a clear sandwich bag and mark it with a felt pen and put the bags in the order they were removed.
If you can't find an oem gasgas bearing or seal just post a picture and someone on the should be able to help you find a replacement. For the most part main bearings and seals should be easy to find. Replace any old seals, gaskets or bearings now and you won't have to go back into the bottom end for a long time.
Don't monkey with the transmission but you can post a few pictures and the transmission gurus here on the board should be able give you an opinion on any wear or needed parts.
https://www.youtube.com/watch?v=kYX-bOG9vR4