If it was me I would have saved all the old metal I cut out, if you haven't already.  I would make a cardboard template of it and start forming it by hand.  As for trying to make a form out of wood, no way it would give you the results you are looking for.  You could never get crisp bends or edges.  You also have to find a way to keep the top part of your wood die aligned with the bottom wood die.  Plus by the time you even tried to make a wood pattern with a top and bottom you could have made the part by hand.

When I replace metal I try to remove only what I need to in order to replace the part I am after.  Far less chance of things getting out of hand.  Second I would always have a point of reference to measure from or to duplicate from a factory part that has not been altered in anyway.  You get to far ahead and you could get lost and end up with things being way off.

So yes if you have parts that are removed and can be replaced I would replace them as long as they do no cause issues with the next part that may need to be removed or installed.

I would cut away the rust and hammer up a piece to fit in. This is not something that shows. If you want a 100% perfect car, you need to go buy one.

If I still had my wrecked 66 it had a perfect top on it.
 

6sally6 wrote:

A 'little' off-topic..........wonder why the factory made that section of the roof with so many "windows" & openings?
Weight savings?!
6s6

 
They add stiffness, prevent “oil canning” and are placed in area’s to prevent wrinkles during the die  forming process.

Rudi wrote:

6sally6 wrote:

A 'little' off-topic..........wonder why the factory made that section of the roof with so many "windows" & openings?
Weight savings?!
6s6

 
They add stiffness, prevent “oil canning” and are placed in area’s to prevent wrinkles during the die forming process.

Weight and cost savings too.  The metal that would have been in the window adds no strength; the strength comes from the folds around the window opening.  However, it still adds weight, even though not a lot, its the old adage about losing weight on a car: don't look for 10 ways to lose 100 lbs, look for 16,000 ways to lose an ounce.  Plus, then they could sell the extra as scrap to be recycled. 

TKOPerformance wrote:

Rudi wrote:

6sally6 wrote:

A 'little' off-topic..........wonder why the factory made that section of the roof with so many "windows" & openings?
Weight savings?!
6s6

 
They add stiffness, prevent “oil canning” and are placed in area’s to prevent wrinkles during the die forming process.

Weight and cost savings too.  The metal that would have been in the window adds no strength; the strength comes from the folds around the window opening.  However, it still adds weight, even though not a lot, its the old adage about losing weight on a car: don't look for 10 ways to lose 100 lbs, look for 16,000 ways to lose an ounce.  Plus, then they could sell the extra as scrap to be recycled. 

 
How would adding a inverted piece to the window and spot welded along window flange?

Best way I can describe is a brimmed hat attached at edges to existing opening.
There would be a small channel between the two pieces.