Hi--
I just replaced mine, and here's what I did:
The lower boot fits into a slot machined around the lower shift lever mount. It should hold in place, although I have been told that for later model cars this boot was eliminated.
I placed the rubber spacer above the shift plate, and it is held in place by the molded nylon mounting plate. Maybe I did mine incorrectly, but the transmission seems to shift just fine.
Joe