I'm going to wager a guess and say that the most economical way to replace the top, full/quarter tonneau, and the side curtains would be to purchase them from VS. Kirk has the patterns and he probably has them made in-house but I don't know that for a fact. However, you are in a unique position of having the new pieces made EXACTLY to your specifications.
There is one current/active thread and several other past threads regarding the fit of a stock top in relation to how it covers the side curtain. Others on here have posted about how they have added material to the side curtains or the top to extend the coverage. A competent shop could easily source the Sta-fast material as that is a name brand if memory serves me correctly. A pattern could be made from the pieces you have and the new pieces custom made. Instead of a plastic rear window and plastic side curtains you could have glass or plexi-glass windows sewn in. You could also do a contrasting stitch color. You have your choice of black colors since not all of them are the same. You could add some height to the top by lengthening your bows, level it by shortening the rear bow, or anything else you can come up with. You're going to pay more but you're in a position to get truly custom made pieces that fit exactly to your Speedster.
You could also call Kirk and ask if you could buy the necessary pieces i.e. the side curtain hardware, front windshield cap, and latches instead of cutting up your current pieces and reusing the pieces. That way you could sell your current top/side curtains/ and tonneau.
If you want it exactly how it is now but in black then go to the source...VS.