Alright, after 9 hours of downloading, intense troubleshooting and all I finally found what was wrong with my installation.
It seems like some files in the pso2_bin folder have not been assigned the proper permissions to be overwritten by the launcher to be updated. That resulted in the 5-6 files at the end of the patching process to come out with the error. (Most notibly the 'otp_notice_na.rtf' file)
When using Auracks tutorial and assigning the ownerships to me for these particular files and redoing the patching process by choosing 'Check Files' in the launcher, it went through without any hitches and I could log into the game and play. (Just tested logging into my character I started on Xbox and running around the lobby, but that worked just fine)