Can't get DS door gapped and aligned properly- gap is too big or body lines don't match.

[elwood]

Lots of times aftermarket parts are not an exact weld in replacement. They need adjusting and tinkered with.

 

[DATEC]

Do you have the weight on the suspension (wheels on, on the ground) or are you doing this with the car on jack stands?
If on jack stands that is never a good idea, the car will flex and you will have a mess on your hands.

 

[Dean Jenkins]

I have a 69 El Camino numbers matching SS 396. It is at a body shop for quarters and a roof panel(vinyl top ate the roof). They tell me the quarters and the roof panel doesn't fit correctly. They are not offering to tell me what is wrong. They are Goodmark Panels. Could that be the problem. I am going to see it tomorrow. The panels are not attached to the Camino to my knowledge. I know this is presumptuous but anything I should be looking for. I may just pull the car and learn on my own.

Not presumptuous at all. Everyone is here to learn and help.
The shop saying the panels don't fit is kind of a red flag for me. Any shop that has experience with this type of work should be fully aware that reproduction panels rarely fit and need work, sometimes a lot, to get right.
If they are saying the panels don't fit, that implies that they have cut the old ones off and tried fitting the new ones.
If so, it would be really hard to move the car in that state.
I guess I'd ask them what the plan is and go from there.

The pro's here probably have more, better insights.