a) create a simple theme embed your flash files in there
b) for my needs i used the content module, and added all the basic content of the previous site (creating the right block menu structure from within the module as well)
c) changed the flash links with the correct urls (if you can pass variables to the flash menu, you can pass the selected content item id on every page load to the flash file and highlite the current menu item for example)
d) i also used xnews
i dont think you will have problems implementing your site's structure and layout using xoops, but i think some experience on xoops will help you get over with it much quicker.
Whatever happens though, we will be here (hopefully) to help. :)