So it seems that the hinges are the problem, you need to see if somehow when they've been fitted that either they have failed themselves somehow or the body has made them twist against each other
You need to maybe hold the door up /support it and then undo 1 of the hinges and see if that hinge is then free.
It'll either allow both hinges to seat freely and solve the problem or show 1 or both hinges to be faulty and I'd say an odd manufacturing defect has occurred.
You may want to ask Ford if it is a known problem.
Not something I've read.
56 350 2.2 130ps mk7 with 2 side doors
65 290 2.2 125ps custom with 2 side doors
07 350 170ps
Ids v86 licence + v86.04 update + xprog
hereIds map
here