I think I might have figured something out, but I'm not sure what.
I removed the outer shell and aligned only the inner shell with the fore and aft index holes. Looking at the inner shell from the inside, those holes appear to be correct because the inner shell is square in the door opening, so I've got some confidence in those.
The next thing I did was duct tape the inner shell to the cabin top so I could remove the clecos and be able to "slide" the outer shell around until I could get the best possible fit. AKA: Ignoring the index holes in the outer shell completely.
(Which by the way were drilled by a drunk money because none of them align and when you measure them with a tape measure they're off by .25-.75 inches from their counterpart holes in the opposite shell.)
The first three times I aligned the outer shell, I ended up exactly in the same holes where I started. As I slid the outer shell around, I began to grow some confidence that the aft index hole was drilled before the monkey reached into the cooler for another. So I cleco'd the aft hole and essentially pivoted the outer shell around that hole. I seemed to find a sweet spot just slightly off from the previous position. It's not perfect, but better.
What it basically did was remove the gap from the compound curve located on the leading edge that Rick mentioned, but it opened a new one on the aft edge. The aft edge is pretty flat and ironing out the wrinkle becomes much easier when you remove the compound curve component. It's much easier to get the two flat surfaces to comfortably squeeze together.
I'm still not happy with it but I think it's something I can live with. We'll see what I think about it tomorrow morning when I take a look at it with a fresh set of eyes.
Van's doors really do suck.
The folks who have gone before me weren't lying. (Like I had hoped.)