Managed to fix it though. I carbon copy cloned my main hard drive to make a new, then did a clean install of Mountain Lion. This took a download of Mountain Lion from the app store and Lion Diskmaker 2, which installed a full version onto a USB stick. I then did a clean install. This is of course after de-activating Adobe CS6, Final Draft and AVID Media Composer.
Just to try it, I had it import my User and Applications from my carbon copy cloner version (thinking this would bring over the problems, whatever they were), but after the import I had a system that was working fine, with all of my applications installed. Sure I had re-install a few, but overall everything worked just fine and my computer is back to speed!
I am glad there is still a way to do a clean system install, since Apple removed the Archive and Install option a while back. Still it should be easier than it is (IE the option given from Apple). Glad it is working though.
Now just really need a bigger hard drive so I can get my Time Machine going again (had to do a bunch of moving of files to get an extra drive for the Clone procedure).