The door obviously needs to go directly upwards, filing the holes is an option, but eventually the shoulder of the bolt will foul on the hinge recess.... not the best solution! try this instead, assuming that your front door is correctly adjusted and your happy with the gap to the front wing, Firstly, remove the "striker" pin on the D post (inside door shut, nearest the rear wheel) doors should be hung, and gapped without these fitted to give a true reading,
Next, unbolt and remove rear door from the car, then its time to get the tape measure out! hang the tape on the TOP of the top hinge, and measure down, to the top face of the bottom hinge, lets say it measures 300mm between the hinges (example)
Looking at your pics, I would say that your door needs lifting by 3mm, you now need to use a sledge hammer, to persuade the top hinge upwards, so that the measurement will then read 303mm, once this is achieved, you can then adjust the bottom hinge in the same way to bring the measurement back to 300mm, its that easy! refit your door and striker pin, and see what you've got, it should be there or thereabouts, final adjustments can be made by shifting the striker pins about
Using a sledge hammer like that may seem a little extreme, but its really the only way to do it, get someone to hold a cloth or the like around the B post if you dont trust your accuracy! 2/3 sharp blows should do the trick...
Hope this helps
Tom
