Okay, I tried the test of unplugging the maf and running the car and this is what I have found.
When I unplugged the mad and start the car which was already warmed up the afr were locked at 14.7 andthe car ran smooth as can be. However after about 45 seconds then the car comes out of what I assume to be a sort of warm up closed loop and the afr starts to change up and down then the car started to run rough again.
Then I shut the car off plugged the maf back in and started the car again. Again the afr is locked at 14.7 and runs smooth as can be until it comes out of that warm up cycle and the afr start to fluctuate and then its almost instant it starts to run rough. So maf plugged in or unplugged there is no difference.
However I feel like I am getting closer to the problem with the roughness starting as soon as the afr's can fluctuate. But at this point I'm not really sure where to look next.