...I'm no expert, but I can tell you what I did and how it came out.
It came out looking great, but that's just my opinion, and it did take a lot of time.
The door gap where you have the pencil arrows, at the top curve of the fender, needs to have the most space. When the door opens, it has to move past the fender edge without scraping off paint. Your gaps look fine, although the door/fender edge does seem to be uneven/inconsistent. The door (skin) edge is rolled onto the door frame. If you take some masking tape (or a fine line marker), you can lay out a more consistent line/gap that you would like it to be. Then you can remove the door, and use a hammer/dolly to roll the edge where you want it (assuming you can only move it towards the back -a larger gap). You can do the same with the edge of the fender (moving it forward). If you hammer it too much, or move it too far, the sheet metal will crack or separate. Then you have to carefully weld it back together, grind and reshape it. I used some plastic tile spacers to check all the gaps (all the way around) because you can't trust your eyes -or at least I can't trust mine.
The door bottom to outer sill can be moved with a block of wood and a BFH. It helps if you use a jack, or two to support places you don't want to move. I have a pre-60K, so my sills and door bottoms are curved (top to bottom and front to back) while the post-60K are more flat (front to back). I did not try to curve the new sill, instead, I matched the door to the sill (some bending and some filler). Once again, a block of wood can be hammered into the corner at the top of the sill and significant movement is possible. When it's all done, a skim coat of filler can hide the hammer marks (assuming they are not too big).
I see something on your car that looks like mine. Take a straight edge, and lay it down the B-post, where the sill is closest to the dog-leg (where the rear edge of the door closes). You need to be sure that outside line is straight all the way to the bottom of the sill. My dog-leg repair wasn't done exactly straight, and I didn't notice it until after it was painted. (Much too late.)
I used 3M seam sealer to close the gap between the sill and the dog-leg. It's supposed to remain flexible, but can be painted. It took several coats of primer to get it to look smooth, but I like the way it turned out. Many prefer to let that gap open.
Another thing to remember about door gaps is the amount of movement they might have after everything is together. By movement, I mean the door is closed and latched, but the flexing of the tub (whilst spirited driving) will create relative door movement. You should be able to pull the door up and down as much as the hinge will allow, without the edges of the door hitting the fender, cowl or b-post. -The latch can be set to disallow most downward movement, but it should be easy to open/close even if its on an incline.