Please keep in mind if your hinges are good (no play, no wiggle and rebuilt keeping the same pin location) a tiny difference in adjustment at the hinge end side can make a notably larger difference at the latch end side. A little movement is often all that's needed. Usually what I'll do is get the doors installed as you've done and then loosen them at the hinges and holding my finger down there to feel move the door in/out just a mm or so, tighten and try that. Also...if your door sits in or out (from the body) at the latch end you may either have to bend the hinge (the part which fits into the door) or in some cases you can either use shims on the back side of the hinge or file the hinge bolt holes a bit to make the difference you need. If you draw this on paper it is easy to see what I mean. The long part of the hinge that fits into the door will often either need the far end of it moved out or in to make the door sit right.
And I have seen doors where the cab had to be "adjusted" to make the body lines and door lines match correctly. This happens when the mounting pads either shrink/deteriorate or are replaced with some that are too thick or the rear mounting grommets have worn out, causing the same thing. Essentially the body flexes enough (front to rear) to make the door opening a bit wonky. It may not sound like this should happen but it can. In this case it is pretty close to impossible to correct it with adjustment. Good luck!
