Here's an update on situation; I finally managed to get the remaining three titles going, though it's a little laughable.
To re-confirm the accuracy of the situation, I've decided to re-obtain fresh copies of the games itself and try again. First step, without any form of modification I tested them on my PSP, using the M33 driver.
Initially, both Persona and Disgaea 2 didn't work, as expected, but Naruto actually ran without any changes to it. Surprise, surprise.
Next, I did the same process mentioned in the first post, with an additional step; once I extracted the EBOOT.BIN, I selected 'File' - 'Filelist' - 'Export' and save it in as 'Filename.txt'.
Once the EBOOT.BIN is decrypted, I went through the remaining process except when before saving the changes I selected 'File' - 'Filelist' - 'Import' and chose the text file I've just saved earlier. You'll be prompted a confirmation window but just simply select 'YES' would do.
Then, I tried testing the other 2 titles again. This time, both games were able to run except for the exception of Persona, in which right after the introduction video I was introduced to a black screen and it refused to budge.
I went back to the main menu and changed my driver to the 'Sony NP9660' and tried again and finally Persona was able to get to the main screen and past the new game selection. However, I have yet to fully check the gameplay functionality of the games so there might be some hiccups in-between. When that happens, I'll let you guys know.
A quick shout-out to the folks here that offer a hand when I was asking for help. Thanks alot, guys.