A 2011+ SHOULD have the correct pinion flange already. I have heard of one person though who supposedly got a 2012 from Roush and had to change the pinion flange.
There is a write up sticky over at mustangcollective.com that goes through the steps (including pinion flange swap if a 2005-10 rear end is used).
Pretty easy if you have a 2011+ with the correct pinion flange. Unbolt the driveshaft, take off the caliper (hold it up out of the way with wire, no need to remove it completely), unbolt the bottom of the shocks, unbolt your LCA's, unbolt the UCA and the rear end will drop out. Then you just reverse the process with your new 8.8. They are heavy so have some muscle on hand and a good tranny jack to move the rear ends out and back in.