Even for a rookie I even impressed myself, when I started down this path I wasn't sure it was even feasible, ended up being a lot easier that I thought it was going to be.
It looks like my registration is finally resolved. CHP did their VIN check and I got the paperwork through DMV. So if I need to transport the car I can tow it on its own wheels or use a dolly, once I receive the registration back from Sacramento I can use the plates but till then I have to use the temp (which is temporarily affixed to the car, will use better tape if I end up moving the car before then.)
Soon as I got back from the DMV I went at the rear window some more. Because of the amount of effort it takes to get the section in and out I chose to trim all the edges down and round some corners. Before I pulled it out from the previous fitment I looked at where the interferences were, after trimming several areas and removing some metal that wasn't needed I tried the section again. It was easier to drop into the car and wiggle up into place, this time I was able to get it the full extent needed.
Now I need to start tightening up the joints. At this time I have about 3/4" of overlap on the joints with the exception of the drain channel where I set for a butt joint and ended up with gaps. The other edges will be trimmed back further and flanged.