You can definitely put the Cobra Jet Manifold on before you do headers. We call that our 475C package shown here: 2011-14 Mustang GT Brenspeed 475C Package
This will produce 475 flywheel HP with those 4 items. Manifold, 60mm TB, CAI, and the calibration. If you want to do Long Tubes after that you will net about 20-25 flywheel HP which is a solid gain. If you have absolutely no plans to supercharge in the future then the CJ package is the only way to go to maximize your N/A car! It feels like a supercharged 3V.