I think the bolt you are talking about is the "pivot" bolt, for lack of a better name.  It's at the door window side of the vent frame and It's the one bolt that pulls the vent frame tight to the door shell.  As I recall, this bolt uses a notched, dished washer that is bigger than the square hole.
The other bolts, as you no doubt have determined, put the long end into the vent frame and the short end with the attached flat washer pushes back, toward the inside of the car, in the door shell.
With the first bolt snug but not tight, you can adjust the transverse and longitudinal, and forward/back position of the vent frame.  Once you get it where all is well you can tighten, but not over tighten, the first bolt.
If I forgot something...likely...maybe someone will chime in.

If you can't find those funny washers in your pile shoot me a PM.  I went through six doors to get our heap close and I'll be happy to do a little rooting...might even know right where to look.

Good luck.  Doors take time but the results are gratifying.  Don't give up or get in a hurry.

BB

Well I could not dig them up, so being a machinist I made a couple of square nuts up. Worked out good. Thanks for the help though.