Thanks Joe, you’re right and that’s exactly why all this mockup work is being done to catch this kind of stuff.
After the “SLIGHTLY OUT OF ALIGNMENT!!!” moment it was decided to triple-check the side glass again. Especially the right-side glass including the upper weatherstripping on both sides this time. Kelly found the same thing that I did, it just fits without much adjustment on that side. The good news is it looks perfect and will function fine and shouldn’t cause any issues.
Decided to grab the inner fender wells from the body shop. Thought if I predrilled the tiny holes, it might make installing the splash shields staples easier (?) when they come back painted.