A few years ago I looked at FMP 8 and 9, but there didn't seem to be any 'upgrade' path at the time without completely redoing the database,
Actually, FileMaker 8 and 9 could also convert FileMaker 6 to the .fp7 format.
This is the file I use to open FMP 11. It is VERY slow to open, like minutes. On top of that, it can not find the other related databases, such as the Preferences database or many others.
This is probably why it is so slow to open, it is searching through many external data source references to try, unsuccessfully to open the files that they refer to.
Open Manage | External Data Sources. Use the window that appears to edit each external data source reference so that it correctly "points to" an existing file. Do to the sloppy way older versions of FileMaker managed external data source references, you likly will find more than one external data source reference to the same file. Make sure all such references work and modify any that use asterisks so that the refer to the correct file without asterisks (They really, really slow down how fast your file opens). Don't delete any unless you first carefully and full determine that the reference is not actually used anymore. (About the only practical way to do this is to purchase FileMaker Advanced so that you can generate and analyze a Database Design report for instances where a part of your database uses that external data source reference.
Since you have multiple files, you'll need to do this for each file as each file has its own set of external data souce references.
This should result in files that open much quicker and eliminate all dialogs that have been popping up and asking you to find the file.
I'm working on that now, I'll let you know how it goes.