I'm only a few years beyond my rebuild, but have always been disappointed that my green Willys leaked. I pulled the drive train, determined to seal it up better than the first time around. I was surprised how greasy the shift tower was when I pulled it to drop the tranny. I decided to decrease the chance that this will leak. I added a seal plate to the rear of the shift rods. I've seen others do this with some success. I drilled and tapped the tower (1/4" x 20) so I could hold the plate in place. I added some RTV gasket maker.

I was missing one of the caps on the front of the shift rods too. I wanted to get it all back together today, so I was a little bummed. Turns out, 1/2" copper caps are a perfect fit. I shortened them, added some Permatex, then drove them in. A perfectly workable solution...

The jury is out as to whether these steps will help seal it up, but it's a relatively easy approach, so it may be worth a try.
Tim