I don't have the steam version so I can't say for sure that its possible at all for this to work but I have the non steam version and I have the 3 persistent game data files but there is another set of files that you most likely need. It depends on what folder you have BoI in but you should be able to do a search for "Binding of Isaac" which will pop up a second folder that contains more of the files. For example, this is the path to the persistent game data "C:\Users\Jake\Documents\My Games\Binding of Isaac Rebirth" and this is the path (on my computer) to the second folder that has the necessary files "C:\Games\The Binding of Isaac Rebirth\". If you can't find the specific files you need, you may just need to copy and overwrite any of the files in the steam version that the non steam one also has. Essentially, guess and check is the only real way, being that the steam and non steam version will be different thanks to the steam specific files.