Set it to "flat" (parallel to the window, ignore the gap for now).
Then, as noted in a few prior posts, check to see if you can adjust the frame mounts. (3 bolts to the body down in the well area, need to remove rear inner 1/4's to access them). They are just visible on the right in this photo, can't find a better one of that area from my resto pics.
This may be the issue. As you note the side rail adjusts 1/2" it would appear the adjustment is correct but that the frame on that side is sitting too high or too low. Drop the windows and you can check level and alignment with some floor-to-frame or jamb-to-frame measurements on both sides with them set in a similar alignment to the glass edge to confirm symmetry.
If the eccentric is worn they are not reproduced and you need to find a donor car/frame to part out... but from the level of adjustment that seems unlikely.
"True terror is to wake up one morning and discover that your high school class is running the country."
8R03S : 76A I 2A 15M 72 5 U
8R01S : 65A B 2A 28M 72 7 5 - Factory GT
8R01C : 65A M 2A 01E 72 2 W - CS/GT
8F01X : 65A I 2G 20E 24 1 U - EXP500 repli-bute