09+ VVT and MDS bypass?

What engine management are you going to be using? If you're using the stock computer there's no need to do anything to the vvt unless you're going to run a bigger cam and need a limiter. If you're going to an aftermarket ecu (Holley, Megasquirt, FAST, etc), you need to lock the cam phaser with the comp cams kit and then figure out a way to degree the cam since no adjustable timing set is available.

I have a 2010 5.7 running on Holley EFI with the cam locked out and couldn't be happier. What direction you go really depends on what you're looking to get out of it and what your goals/skills are. And what your time is worth.