Russ,
I did try my rear window glass on my '70 RR this weekend. The glass is from ECS. To recall, I have replaced the roof skin, both quarters (factory style) and the Dutchman panel. So everything around the glass has been replaced. I have an install kit that has (4) rubber blocks and the black goo seal strip. So where to begin......
Like you, I find that the part near the lower corners dips down too much and almost hits the metal. Like less than 1/32"!!! But my corners don't flare up as much as yours. So what I am going to do is use rubber pads cut from a rubber sheet to shim the glass around the perimeter. I have several different thicknesses of sheet I will use to ensure that none of the glass will be touching the metal frame and also hopefully maintain an even height for the trim. Then with the rubber pads in place, I will use the goo to seal the glass to the frame. I don't really trust the goo to be able to hold the glass in place considering how close it is to the metal.
You can buy EPDM rubber sheet from McMaster Carr. If you don't know about them, you should. It is like a candy store for me.
https://www.mcmaster.com/
I will keep you up to date with how things are proceeding. While I am sorry you have been put through the wringer on this, you sure saved my ass by bringing the topic up.