Hi John,
you're taking something absurdly simple, and making it complicated.
I recommend you start again. Remove fm3 from your app completely - delete the upg.tps files, remove your embed code.
Then
a) add the Fm3 global extension.
b) do not do anything else.
Specifically do not add the Runtime File Manager procedure. You cannot use that via a web interface.
(Aside: The reason you got the error with the MessageBoxLogfile, which is in the RuntimeFileManager screen, is because you have the RTFM screen set to use all the files in the dict, but you are not generating all the files in your dict in this application.)
You do not need (nor I think want) multiple upg files. A single upg file will suffice.
In the longer run you will want to create a separate exe, which runs through all the data sets, opening all the files therein. This will allow you to upgrade all the files after an upgrade, without waiting for the user to access a file. Much better from a performance point of view to do the upgrade when the user isn't waiting. But that's down the road and not something you need to worry about now.
Cheers
Bruce