Unfortunately you cannot use the '96 booster. The brake arm is straight and may pose alignment issues when connecting to the brake pedal and cause bind. The correct and only booster you should use would be from a 1994-1995 Mustang or a 1993 cobra. 1993 cobra would be the most direct bolt in since the mounting bolt pattern is the same as the fox booster.
As for using the 94-95 Cobra MC...you can, but the fitting nuts are reversed. Reason you don't see a lot of people using them is because you'll need the MC and the brake lines off a 94-95 cobra that connect the MC to the prop valve. Prob is the cobras are ABS, so there is no direct swap. You would need to track down the correct metric fittings, and make your own lines from the prop valve to the MC basically.
However, it is your best swap at keeping the stock booster, but in terms of which is more of a PITA..i would say the booster swap would be easier. More than likely you will need to change it. But you can try it out and see how you like.
But i can garantee you the 96 MC will give you a stiff pedal with the stock booster. My first drive with stock booster and 1 1/16" MC gave me a pedal so hard i could barely stop from 30MPH without two feet on the pedal.
I swapped the SN95 booster in and it was driveable, but i could not lock the wheels up and the pedal was still firm. So i ditched the 1 1/16" MC for the Cobra MC and all was good!
The resevior can be swapped between the MC's. I beleive it is the same part. up til 1998.
Keep in mind there are two different Cobra calipers. The 94-98 38mm units, and the 99+ 40mm units. The above site was written before the 40mm units came out.