YES! If you are using a stock
Vortech kit "right out of the box", YES the stock MAF will fit. The Vortech supercharger kit is designed to fit, and the provided FMU is calibrated to run on a STOCK Mustang engine with STOCK parts. The dryer pipe assembly actually works better with the stock MAF because a larger aftermarket MAF may or my not fit in it. (Mine did not)
If you are installing that kit on an unstock engine or make any other mods to that engine it all goes out the door. Time for a retune.
After its all said and done you will STILL be required to find a local Dyno near you to have it properly tuned.
I learned years ago that if/when you buy a supercharger kit for your Mustang go ahead and plan to set aside another $1000-$1500 in supporting parts. That doesn't include a powerpipe. A powerpipe is a choice and is not required to make power.
Anyway, congrats and when your done you're gonna have alot of fun with it.
Ask me how I know