Well Indian Wells and Miami are best of 3 set finals now so will this be the same on clay??

If it is then Federer would have a better chance of beating nadal on the surface IMO.

i think you're right, but i don't think it's just a physical thing, i think it's as much mental. Fed's stamina is superb, of course Nadals is, but Nadal has built his reputation on tenacity, he gets in his opponents head.