You make good points.
I personally hope he doesn't leave Rooney up front by himself. Its definately a tough one because Barca's midfield could run riot if he does play the 4-4-2, but I think he has to play Roony and hernandez. Its served us well this year, and its quite a negative message to send out if he does'nt imo.
Taking everything into consideration though, i would go with the 4-4-2, but with Rooney playing a bit deeper so he can drop back and help out in the midfield, when needed. Also I agree, put Park on the left to help track back and have valencia on the other side doing the same. I'd probably go with Giggs and Fletcher in the middle. Giggs has been amazing this year and his experience could be vital, with fletcher there to get stuck into Messi (or at least try lol).
I think there is no questioning Barca will have more possesion and territorial advantage. I hope SAF will tell them to stay strong, keep their shape, but not be scared to attack when we can.