I just did this last weekend on my 69. The lower boot goes through the floor from the top. Which means it bolts from the top instead of from the bottom as the manual may imply. The screws go through both boots from the top and attach to the retainer plate that is welded to the underside of car.
When I put mine together, I had the shifter off the transmission. I dropped the lower boot in from the top and temporarily put the top 4 screws in to hold it. I dropped the shifter in from the top and bolted it in place. I then removed the 4 screws for the boot, put the upper boot in place and tightened it all down.
I think I might have not routed the reverse light switch wires correctly though. I just had them come out the slit in the back. I wonder of they come out the extra slit that is on top of the transmission.