As far as file replacement, the Legend of Dragoon hacks do a neat trick in that you need to extract the relevant file from both versions for it to work. The patcher would then work it's magic and you'd put the file back into the US disc. I don't know what's keeping a PSP game from doing that right though.
Also keep in mind that you may or may not need to make some sacrifices in the undub; the original music patch hit a few rough spots too.
I already extracted the files from the Japanese ISO and US ISO, my problem seems to be inserting the Japanese files into the US ISO without it causing problems that either result in nothing which means the file doesn't register or a crash.
Some PSP games use some kind of LBA or file size protection. It either checks if those are untouched or simply assume they are, so if you change it it won't work anymore. You can try replacing files with umd-replace (http://www.romhacking.net/utilities/891/) padding the smaller files with zeros to match the same file size as the original and see if that works. If you want to use bigger files you'll probably have to use a debugger to figure out how the protection works and disable it.
It's also possible that there's some hidden files in the ISO (not on the standard file table).
Have you seen this thread?
I didn't know that, maybe that's the problem, could I alter the LBA in anyway to accommodate the new files or is this not possible?
I also tried that tool but doesn't do the same as replacing the files directly with UMD Gen? Also I couldn't get the program to detect the file in the ISO since it always says "file not found in umd image", I'm not quite sure what I'm doing wrong.
There is a possibility there is hidden files but if it does have some then I'm unsure how to find them.
I am aware that there is a that patch that Canzah made but he said himself that it was unfinished and not done very well and I'm hoping through a lot of struggling to remedy that and have a proper undub and music hack to add to the collection of undubbed Persona games on the PSP.
Here is also the file list opened in umd gen.