If you've managed to extract and edit the files, then no need to bother anymore. Find the edited files and apply them as a game patch using Luma's LayeredFS, it will have the exact same effect, only different thing is that you get the option to turn the patch on and off in case you want the vanilla game!
About the files not having the edits, did you make sure to save the changes you made to them at every part? Also, check the automatic backups created by PK3DS in case the edited files are there, will save you time when re-editing.