Do you actually have a copy of the original 1.3.9 database from before the upgrade? If you do, drop all tables in the 1.5.4, import the 1.3.9 DB into the 1.5.4 database, then run the zcinstaller and process the DB upgrade. That will update your database from 1.3.9 to 1.5.4....now the only problem you are going to have is if when building out the 1.5.4 you ran sql files for addon modules, parts/pieces of them maybe present if those modules were installed in the 1.3.9 but if you try and run some of them again to put them in you will most likely run into mysql error for stuff already being present. That's a slightly harder nut to crack, as it requires knowledge of how to work in phpmyadmin to pull configs out of the configurations table based on the group_id, copy those out, and delete them, then you can run the sql file to add the newer version back in and you can then make any adjustments to setting from inside the admin based on what you copied out and set aside.....confused yet? It does take patience and attention to detail to not screw it up. but its the kind of thing I run into again and again while doing upgrades.
If you had started out correctly by doing the upgrade on the original database you would have been better off and would only have to copy over those customers and orders that were new since you started working on the upgrade.