Got the car back just before Memorial Day weekend and happy to report that it was properly repaired. I'm very satisfied with the second shop's work and willingness to help me -- a couple shops turned me down when I told them it was supplemental repairs and I certainly can't blame them. One of those shops did refer me to the one who ended up doing the repairs, and I'm very appreciative of that.
Not only was the new shop more communicative, but they advocated on my behalf against the prior shop and did everything by the book per Ford's repair standards, documenting it all along the way. The panel gaps are all identifical to the passenger side and the doors open and close properly. All of the trim lines up and mirrors the opposite side. All in, they ended up doing approximately $4k in supplemental repairs, including additional pulls at the B-pillar, which fortunately was not damaged beyond the exterior layer.
The original shop was on the line for those repairs and had to cut me a check which I picked up from them. I sure they're not my biggest fan but I did not trust that they were ever going complete the repairs properly.
In total, we spent over 4.5 months getting repairs completed, and now we still have ongoing issues with insurance, but I'll leave those details out until we get that resolved.
Just happy to have the car back. Had the new rear window tinted yesterday to match the others and added 70% 3M Ceramic IR to the front windshield as well to help keep things cool inside. So far really liking the front windshield tint - first time I've done it and it doesn't look any darker but there's signifcantly less eye strain without sunglasses on. I hate when the sun reflects off chrome interior trim into my eyes on long highway drives and I'm hoping this helps with that.
Thanks everyone for your advocacy. Looking forward to continuing to post on here, hopefully regarding mods and a tune, not damage repairs.