After the purchase I get all the working files?
Yes. After the purchase you get all the files used
(actionscript,fla,xml,php,js,html,used pictures etc)
Can I change the menu structure in the “flash site template” ?
The order of menu items can be anything. You can change it yourself in the xml file.
Each template (template gallery, template text, flip book) can be used many times in the menu.