Gary and Doug, thanks for your reply. I finally realized that this may have happened because I was tying to “organize” files on my hard drive over the past week. In doing so I had changed the name of my website folder from “Website” to “10 Website” in order to get the folder to appear closer to the top of the finder window. The timing of this problem happening following the RapidWeaver update may have just been a coincidence.
It seems odd to me though that RapidWeaver was looking for 60 files many of which were no longer being used and were in the trash. It was also in many cases asking for the same file multiple times. In the case of my banner it was looking for every variation of the banner photo I had tried and discarded before publishing the website with a new theme a month ago. That really makes no sense!
Anyway, after a few hours of work I was not planning on, I think I have everything up and running again.