Ok, chalk this one up to my MySQL learning curve (I come from SQL Server/SQLite--the file storage structure of MySQL/InnoDB is really foreign to me).
Your advice to clear databases before restoring was right on point--I just didn't understand that in MySQL world, that didn't mean firing up the database engine, disassocating the objects from the database store, then shutting the works all down again [as you'd do in SQL Server or the like]). Instead, it just meant delete all pre-existing .idb files from the data store folder before restoring the file backup! (Thumps head against desk)
Since I wasn't clearing files (and I was simultaneously assuming that my backup program was restoring folders to their same state instead of leaving existing files while copying/replacing old ones in the directory), I was on a slippery slope toward database schema corruption hell. As soon as I deleted the appropriate data folders, then restored (telling Acronis [my backup program] to restore original privileges) all was well.
Thanks for your help, guys--sometimes when you're this new to an environment, it takes a while to get your bearings!
-Pete