Emmit,
I had a similar problem converting from 2003 to 2004. The source control provider that I am using is Visual SourceSafe. After I checked everything into source control and tried to open the project, I was prompted to do the conversion again. No matter what I did, the message would not stop.
Finally I found a post on these forums that pointed me in the right direction. Basically the .csproj.vspscc was missing the "ORIGINAL_PROJECT_FILE_PATH" path. Once I changed those, the solution would load.
http://forums.asp.net/thread/1273192.aspx
I am not familiar with how ClearCase deals with project files. So I hope that my experience will help you out.
Brian