I have played Empire Earth 2 in the past via a disc based version on a different pc some years ago so when I opened it up what I was not expecting was for the mouse to be offset especially noticeable at the top and bottom of the screen where it is nearly impossible to do anything, on top of that the screen is not displaying in fullscreen mode unlike EE1 and EE3 it will only run properly (not including settings) if at only half screen size. Any help as to possible fixes

I think it's the screen resolution problem.
You can try Unofficial Patch 1,5, with support for all screen resolutions, and fully-working fullscreen mode:
http://www.ee2.eu/t1723-ee2-1.5