Hi,
I think the idea of a windows setup.exe is a good one, I do something similar myself, http://www.kicchip.co.uk/download/arduino/1.0.1/setup.exe but yours seems to have more features than mine.
One reason I used an installer was so that the installation path could be stored in the windows registry, that way my other software knows where to look for all the arduino related files. Is that a feature you could add to your setup so I could use yours instead?
P.S I use inno for my setup.