I'm trying to get the side windows adjusted. I have gaps I can't seem to close shown by the arrows:

Click to view attachment

I have later doors on an early car. The windows are the correct ones for the late doors.
Here is an image for reference:
Click to view attachment

A and B will rotate the window a little and raise it up and down.
Loosening D will allow me to rotate the vertical chrome piece around C. This allows for the window to rotate and move fore and aft.
E allows the window to move fore and aft.
I have tried all combinations I can think of to move the window where it should be. I should note that the doors are not perfectly aligned, but they are very close. But the gaps are too big to be caused by the doors not being aligned. I've looked at other cars and I've placed my components in about the same places and the gaps are way too big.

The window is seated all the way in the track. I can move it a little fore and aft, but I don't want to rotate it because then it won't be bottomed out in the track. I just reused the rubber U-channel and did not glue it or the window in with butyl.

Is there something I'm missing? Could the window glass be wrong?

I painted the car recently and am putting it back together. I think the car was in an accident many many years ago. It was expertly repaired, but it had a late and early door. It never really fit well before I painted the car; there were gaps in the windows, but they weren't that bad and I attributed them to worn seals. I got a later door from another car so I'd have two of the same. This may be partly to blame.

Between your E and the crank handle there is a height limit adjustment.
Two 10mm wrenches ....
The front corner of the roof looks to have a void at the windshield seal.

You need a late roof to match the late doors. I had the same problem.

I forgot to include that adjustment. The problem isn't height, but that uneven gap. The window needs to somehow rotate and/or move forward.

Yes, the void is bigger at the top front then the top back. But when I rotate the window, it hits the molding on the "B" pillar.

Does a late roof have a different interface with the window? Can you take a picture or two and show me your late roof where it meets the window?

Maybe I could add some shim to the channel that holds the horizontal targa-to-window seal that would close the gap? It would have to be wedge-shaped; thicker at the front tapering to thin toward the rear.

My car is in the body shop. If your car is driveable, meet up with someone at a Cars and coffee and try swapping tops for comparison.

You can see there is some adjustment to the top of the triangle window. Looks like 1/4" or a little less. The window should go to the top. That should solve the problem. As far as roofs go there is some variation in the fronts, but the edges should be the same.
Mark