Is there an adjustment for the door gap as up by the door handle it is flush with the body, but down along the bottom it is approximately and 1/8" out further.
What is the protocol in adjusting it, or is there one?

Slipping a shim behind the hinge will make the gap change. It doesn't take much to make a big difference. Take tiny steps and check to see how both the door, window and lock change.

If you run your hand along the edge of the door, it is smooth up by the handle and out a bit towards the bottom. The bottom needs to come in a bit.

How is the gap to the fender? Tkae some photos of both gaps and let's see what you have.

Tough to say without photos, but if it's what I am thinking you need to loosen up the bolts on the lower hinge and push it further to the center on the car. That should bring the bottom closer in. You can also adjust the striker post so that it pulls the bottom in a bit as well.

Its an odd geometry that can fool you.
The door only goes up and down...
By going up you change the gap and the back of the door and make it wider.
Going down makes the gap at the rear of the door smaller.

Feel the top of the door and the top of the front fender...that typically is wrong and the rear gap will never work.

Like Rick said...show some pics so we can help.

rich

I'll try and remember to get some pics of the door tomorrow!

The bottom needs to come in about 3/16" How do I go about adjusting it?
Click to view attachment
Click to view attachment
Click to view attachment

Loosen the hinge bolts and move the door where you need it, tighten the bolts again.
There's plenty of play in the hinges.

If that doesn't get you close, open the door wide and grab the bottom of the door and twist the whole door (bottom in, top out) until it fits.
Same goes for up/down if your gap is uneven between the top and bottom.

It might just be the picture, but looks like your door is sagging a bit as well?

door needs to go up, and then in.

First thing you need to do is adjust the window post so the top is way out and not really touching the windshield when you close the door.

Then adjust the door to close perfectly while you ignore the window opening.

After the door is perfect, adjust the window post to the new setting.

Rich

There are many ways to explain how to adjust that door but first I have a couple questions.

Has the door always been like that?

And can you take a straight on photo of both gaps?

From what I can see in those crooked photos it looks like the door is either in at the top next to the fender or like Rich stated it may be low.

If it's in at the top where it meets the fender loosen the top bolts and only two of the three bottom bolts. This will allow you to slid the top of the door out without loosing the height adjustment. By moving the top of the door out and adjusting the door catch in slightly you will aligning the bottom back edge.

If it is low start by loosing the fasteners and sliding it up to the height of the fender and quarter panel.

This may require removing the door catch on the quarter panel and loosing the vent window assembly to avoid any binding. From there, start moving the door in and out top or bottom to match the fender. Any difference from the fender and quarter panel you will likely be able to split the difference.

From there you can reinstall the latch and adjust and realign the vent window and door glass.

Clear as mud?