Trans rebuilds aren't that hard, but there are really only 2 ways that I can think of getting water in there.
A: having enough water in your bilge to get up to the seals/dip stick.
B: A failed trans cooler.
If you never have that much water in the bilge, then the transcooler should be replaced, if you do then stop, and if you do and are seeing transfluid leaks then you need front/rear seals.
If you are doing the engine you can rebuild the trans, but it might not be needed.
Engine wise I don' thave a source, I've never done one, I've looked at several sources however. Jasper I've come across before,