Did you say you had the rubbers on? I believe it's easier to line the door up if you remove the rubber seal and the door catch. Line the door up, THEN attatch catch and seal
Icky story - I used to think that - then when I got the early that was all original with excedingly flush fitting doors I replaced the seals. While they were off the door fit was all over the place with the top a good half inch further in than the bottom. Being of a one track mind I adjusted it to fit nice without the seal, fitted the seal and the door fit was miles out at the top so I put it back how I found it. Moral of the stoy is the door will bend quite a bit when you shut it without you really noticing and without it making the door hard to close. Sometimes it will be neccessary to have the top (bendiest part) of the door apparently too far in (without a seal) for it to fit right with a seal. Nothing is straightfroward. Now if it isn't quite right in this way without a seal I fit the seal and see what happens.
...yeah need to get a hex bit holder to fit the 3/8 or 1/2 inch drive that would be best way to do other side... Rubbers already glued on as didn't think it would be hard to put something that worked before back on... Doh.. Should have learnt that lesson by now.. But next time
There isn't really a right way and though it's easier (less slamming) to get even gaps around the door and sort out the problems you had without the seal first, it's not the only way and would probably need further tweeking once the seal is fitted anyway. What it does do is allow you to carefully not quite shut the door and after you've chipped the paint on one like you have, you don't do that again! The biggest problem I have is stopping people who are wandering past (like a certain painter I have used) from shutting the buggers and chipping paint before you've adjusted them.
And then you fit a roofrack and it cuts grooves in the seal at the top of the door ... Just as well new doors are unobtanium because they seemed to be slightly bigger than originals - the guys who fitted mine ended up having to buckle the door inner skin at the bottom to get it t go in the gap. While the two-section rusty flaps before fitted quite well.
Don't fit one over the cab unless you have big gaps at the top. Most I see are mangling the top of the doors and rubber seals.