I then ran the launcher through MO to check the video option were consistent and they were. I first opened the new vegas launcher by using FalloutNVLauncher.exe, the game auto-detected the graphic settings and then I ran the game, everything worked great.
Then, following the instruction on the STEP guide I proceeded to set up the various external executables to launch through MO (FNVEdit, NVSE,FNVLOD,wrye flash, etc) once that was said and done I decided to test everything so far was working correctly. Then, I downloaded the MO 1.3.11 manual installation file and placed the 'ModOrganizer' directory in the root of the New Vegas installation, I also downloaded the 4gb patcher and placed that in the new vegas root directory as well. I uninstalled the game and wiped any leftover with CCleaner and then reinstalled it in the root of my C: hard drive. Over the past few days I decided to replay new vegas and so I reinstalled it along with some mods, I then stumbled across the step guide for it and became aware of MO, downloaded it and it ran without problems, however due to half of my mods being installed manually plus, my game being installed in Program Files (x86) which was causing issues with UAC, I decided to start fresh.