After I play my xbox for about 20min it will shut off and flash yellow and orange (yellow on one side orange on the other). When I take the cover off it doesnt do this, I have a bigger led fan in place of the original one, hot air is blowing out of the back, what could be the problem/solution...

Sometimes a replacement fan can reduce cooling if not installed correctly - what does the CPU/SYSTEM temperatures read on the dashboard when sitting idle, or after playing a game for a while?