So I did some searching on the forum and found that there is a gasket used to shim the fuel filler door hinge mechanism. The original on my car was there, but pretty shot. I made a new gasket and added it along with the original so now the left side of the door doesn't drag on the quarter panel when being opened and closed.

What I'm looking for is if there is a way to adjust the depth of the fuel filler door in relation to the quarter panel when it is closed. It seems to sit into the quarter panel somewhere between 1/8" and 1/4". While there is some adjustments that can be made with the 3 screws that mount it to the car, that only seems to move it up/down and left/right, not in/out. Is there something I'm missing?

Go to the hardware store and buy those little rubber stick on "feet" of the right thickness and stick it to the door lined up with the existing bumpers, that should help space it out some. You can trim them down and get them in clear silicone if you want them to be less obvious.

There's a guy on Facebook that has the gasket cut. I got one from him, maybe two, I don't remember now

Putting a physical blockage around the height gap different may work, but I was hoping that would be a last resort. Thanks for the idea, though.

I made a replacement gasket myself. That doesn't help the depth the door sits in the fender at all from what I have been able to adjust.

The long rear screw has no real adjustment iirc put it in last and it may need to make a different hole. The 2 front ones will let the base move in and out some and that should do the trick. The rubber stopper on the other side has a torx head screw in it to adjust that somewhat as well.
Just keep playing with it and you'll figure it out.

The rubber bumper on the opposite side of the hinge is a screw. You can adjust out there also. If your hinge side is that far off you don’t have something put together right of the filler flange is screwed up. Post a picture of what your working on.

Here are some pictures. I haven't really been able to get it much better. The whole door or whatever it attaches to needs to come out of the car body by almost a quarter of an inch.

That's better than they were new. Back in the day some people replaced them with I believe grandam doors as they use inside the car releases. I'm sure there is a write up here somewhere.

https://www.thirdgen.org/rubbinggasdoor/

Also may be of interest.

Yeah, that looks pretty good. There are a couple screws that you could loosen and see if the hing will come out any further. If not, you would need to ‘clearance’ the hinge area to move it out.

Ive always been able to get it flush/centered by the 3 screws on the mounting base.The key is to hold the base in place while tightening down the screws.Do the two front first, then the rear long one (not too tight on that one).Takes a few tries, but it works for me.

It sounds like my suspicions are confirm and there is not dedicated way to adjust it. You just have to tweak, shim, file, etc. between all available attachments until it is right. Thanks for the help guys.