Thanks for the reply. This is a live site, so I had to fudge it, which I did by incorporating most of the graphic elements into a layered Photoshop file and using that as the background. Instead of using an embedded video player, I had the video poster image open a new page, with the video embedded there. Finally, I made sure that none of the tooltip windows overlapped.
That seems to have gotten me something I can use, but I'm still curious about making ordering work as it's not always possible to design around the overlapping windows.
Is this not a problem you've seen before?
Overall, I'm very enthusiastic about Muse and using it in conjunction with Catalyst to allow clients to do some updating.