Correct, the tower and smaller rear wheel well are covered by one piece first. Then, you put on a second piece that covers the front wheel well. The "riser", behind the seats is installed last.
Yesterday and today I worked on removing scratches from the replacement left door glass I got from @Patcon. I had to order some more discs and powder, so I set it aside for now.
I went to install my tail lights and upon close inspection, determined that one of them needed more sanding and polishing to restore the proper shine to the lenses. After some more effort was expended there, I was able to glue the lenses onto the housings. For that job, I used auto body seam sealer. Seems like and odd thing to use, right? But, the old stuff that I removed from the housings when I pulled the lenses off looked like seam sealer. And, I had good luck with using it once before on the tail lights on my other 240z.
My tail light lenses were in rough shape to start. Lots of pitting and scratches, some of them deep. I bought a small roll of felt from Home Depot and made little pieces to replace those that were originally in the bottom of the assemblies. I guess these are vents... to allow any moisture that finds its way into the assemblies to dry.
While the housing were separate from the lenses, I used a heat gun to attempt to straighten the mounting flanges of the tail lights. These distort over time and prevent the stock rubber gaskets from sealing to the body of the car like they should. When "gluing" the lenses back to the assemblies, there is a need to use clamps (and boards and rags) to clamp the lenses to the housings, and let the sealant cure for 24 hours.
Even with the housing flanges straightened somewhat, I used some self adhesive weather stripping (highly compressible) between the tail light assemblies and the body. These are now air tight - no exhaust fumes will be coming in through this notorious location. While not perfect, the lenses look very nice now.