I am installing a gen 4 camaro dash in my 1969 camaro, so I will be modifying door panels to fit the dash in the car. The last thinig I was going to do was purchase a set of new panels and cut them up when there are plent of stock panes that are being repalced for not much money. I got a set of donor panels for $75 including shipping!! I will be doing some of the same work you are looking at, but I'm probably a few months behind you, so no photos or experience to pass along. My plan was to use stock door panes, and the ones I have are pretty bad, but definitely salvagable. I will be going with electric window motors and I want to update the look of the door panes to match the dash, so I will be sealing up holes and making holes, and changing conours, etc.
If you have an auto paint store around try them, or a West Marine is another option. I'm lucky, I have a professional paint and body supply store about 10 minutes away, unfortunatly they are only open during the week, so it is tough to get to them on their hours. West Marine is my fallback, they are open on weekends, and have TONS of stuff for do-it-yourselfers for that kind of project and products for it.
I have not used it myself for car repairs, but there is a rigid foam product we use for filling cracks and holes for building maintenance at work.
http://greatstuff.dow.com/
Most hardware stores have GreatStuff products, and it runs around $10 a can. I was going to use foam, fiberglass and sheet metal to modify my panels, so foam is a filler for me and the fiberglass will make it smooth for the vinyl to lay over.
Hope this helps.