Sounds to me like you may have picked the wrong shop/person to do your work. If the other work was done properly, and the door was that bad of a fit, it should have been returned. A reproduction door wil likely not fit as good as an original did. Keep in mind though, that an original door did not fit that good in the first place.
I personally do not weld anything in place without test fitting the other parts, and checking measurements. Unfortunately that is not always the case with other people. I have seen many times that "body men" have welded quarterpanel and rockers on, and then hung doors, only to have "fit" problems. They then want to modify doors and fenders to make them fit.
Now you are in a position where you either need to find someone that you have more confidence in, which maybe you should have gone to in the first place, to look at it, or let the guy finish it, and see how it looks.