Steam version is best version to work with ATM (compared to non-Steam).
I've confirmed the VN's core save pointers are mostly resolved with the exception that the Steam's Ep4 content core pointers are different than the non-Steam... so I'm using the Steam versions in the mod update as this is presumed to be the "latest and greatest" of the VN's core file system.
If saves are borked in the future (Ep5+) then we'll deal with it then.
Otherwise something wicked is coming (I also took the liberty of giving the Preferences screen a facelift since it was a bit wonky):
I'll see about adding the "Side Story" to either SanchoGallery or back to the extras as a an additional benefit while I'm porting things over.