Thanks for all the input so far guys. Truth be told I'm really pissed at the car right now so I'm avoiding it. I'm really upset with myself for allowing this problem to happen, but it's easier to take it out on the car
Henry is correct, and I'm quite positive it is the quarter. Here is why:
1. I reskinned the door first with the original quarter on. Looking back at some old pics, it looks as if everything was lined up.
2. I then did the quarter skin. I had the door hung. Why did I not make sure it lined up with the door better? That's all fuzzy. When I was installing the quarter I didn't see what choice I had. I pretty much had to put it down tight against the rocker, which was hard to do. I'm pretty frustrated with myself at this part for not saying 'hm, this doesn't line up to the door well.' In my head I was probably saying 'well, I just must not have the door hung well enough....I'll fix that later!'
3. I had my old body instructor over to help me trouble shoot that door right before I moved to Michigan. We got the door hung on as straight and well as a professional could but we couldn't get the body lines to line up. At that time it was just assumed the quarter was fine. He said about the only way I can see to fix this is put on another quarter skin and try to fit it to the quarter.
4. Now to two weeks ago. I KEEP THE DOOR HANGING so as not to ruin our perfect hang job, and remove the skin. I close door and still I can see the body lines on the original door shell (sans the skin) STILL don't line up to the quarter lines. Not good sign.
5. I test fit the new skin (used a Dynacorn panel and did fit remarkably better than the first door skin I used) but quickly found there really wasn't much adjustment I could do to it. It pretty much HAD to go on one way.
6. Install skin, do a much better job this time around so happy about that but still have same problem.
I think the quarter is sitting just a little high and I'm not seeing a good solution. The tragedy of the situation is I had part of that weld cut back open just not too long ago. Would have been the perfect time to take out the welds on the door jamb and rocker and try to move it down. Now I have the weld all glassed and filled over with three coats of slick sand over it.
Localized surgery: What if I were to strip everything off that weld again back say 2 ft from the door jam, and about 6-8 inches down from the weld. Undo welds on door jamb and rocker. Try to adjust it down and reweld. Or is that just stupid and impossible. I need to get some more pics of up other gaps, like quarter to rocker gap, etc.
I'm also milling around Henry's solution of cutting out the C strip. I just hate to chop up a perfectly good one piece panel...