After waiting on hold for about 25 minutes with Apple Care, they patched me through to a ProApps tech. He explained that the render engine used by motion 2 is a different render engine causing the files to render extreemly slow. He basically told me that I would have to rebuild all my elements and lower thirds from scratch. Yes, it sucks. But at least I know why my 5 min clip went from 20 min export to about 4 hours.
Hope this helps those who had the same problem.