Is there some kind of retainer ring (etc) that holds the inner rubber shifter boot in place...? I see nothing in the parts diagrams. I am guessing that the shifter end gets smeared with grease and then installed with the pin and nylon bushings with the "E" clip. Then the small rubber boot goes over that. But shouldn't there be something that holds it in place...? Help...!

If I'm understanding your question correctly the answer is yes there is a retainer ring that screws on to hold the rubber inner shift boot in place.  If you do not have yours you can either seek out an original one from someone or buy an aftermarket/reproduction such as the one Skillard has.  https://skillard.com/product/datsun-s30-inner-shift-boot-bezel/

I'm assuming you're talking about the little three inch diameter boot that attaches to the transmission? If that's the case, then no... there is no retainer specified.

 

Here's what I was told:
https://www.classiczcars.com/forums/topic/44315-innermost-shifter-boot-any-clamps-holding-in-place/

However... I kinda like the idea of the zip-tie.