Window Adhesive

I'm getting ready to install the rear window in my 1972 Ventura, and i've had to repair the entire window mounting surface. I was not able to match the contour of the original window 100% perfectly, and I'm not sure how big of a deal it is. I'll be using the new style urethane adhesive (as opposed to the old strip caulk GM used back in the day), and I'm sure this car wasn't perfect when it was built. Is an unuequal gap of 1/16"-1/8" okay? Will it bond the window in well enough? Illustration below

It should be fine. Just make sure the glass isn't resting on the metal edge.

The urethane adhesives are quite viscous, I would recommend a powdered caulk gun if you have the means.  The Milwaukee I have made quick work of the 3M window weld when I had to replace the window on a excavator cab for a trade show demo a couple months ago.