We've made changes to the sync code several times since that script was written - it's not impossible for the script to help, but it's a lot less necessary than it was in days past.
In any case, the script is telling you that there are some transactions that aren't connected to your current transaction tree - they're basically orphaned transactions that are just being carried along
You can do the following - under the file menu, export your database to the OmniFocus database format, then select "Revert from database backup", selecting the export file as the one you want to revert to.
(Back Up copies everything in the database file, even those disconnected transactions; export only writes out the transactions that are actually connected to the root. In this case, we want the latter behavior.)
If you do that, and assuming there aren't any stale/duplicate entries in your client files list (accessible from Sync prefs) your database should be about as small as it's going to get. Well, sync all your devices, wait 61 minutes, and sync again. At *that* point, it's as small as it's going to get. :-)