You are going to want at least a 70MM TB and a possibly an 80MM MAF - you are moving a bit of air with a 408. As I've said before, look at Pro-M for your MAF, you can find them used and calibrated to whatever injectors you have.
As for the AFR vs TF - seriously, whatever you get the better deal on is the answer. I'm partial to the Trick Flows and their twisted wedge design, good rockers and dual springs.
I see lots of folks doing their own tuning with a Quarter Horse or a Tweecer but what is wrong with just getting a dyno tune done by a professional? These are Mustang computers, there is nothing new about them and a professional dyno tune shouldn't cost more than $300 - and you are done in an afternoon, no constant tweaking...