I had to start over from scratch unfortunately, wasted my time re-downloading the main GalCivII game instead of playing it. Upon further investigation it appears that the 2.0 patch is indeed imcompatible with the older Retail CD version of GalCivII since it installs into a different folder than what the patch is looking for.
Also I had fun re-installing the game because it kept putting the game on my System drive (C:\), which is a big no-no, my games and apps are on drives D-J, I like to keep a clean system drive, makes backing up the system easier. I corrected this problem by finding the folder options in prefrences and setting the drive paths where I wanted software installed.