Ahhh.....an area that I can add a lot of value as I have run 3.31's, 3.55's and 3.73's all in the same car before S/C and after.
3.31 gears....they suck with a manual transmission. You need to change them. Until you do, you will never truly love your Mustang.
3.73 gears....they are a ton of fun....for a while. With the mods you are planning initially, you will likely love the 3.73's when you are screwing off. Howerver, you won't like them when you are driving on the highway as they will put the engine in a RPM that will drone at highway speeds. You're mileage won't be ruined...remember that you still have 6th gear at 65MPH.
Once you put the S/C on...you will rue the day you installed the 3.73's. 1st gear will go by so quickly it will effectively be useless. Now...if you intend on tracking the car (road course), then the 3.73's with a Supercharger will be great as the combination in 3rd gear will be killer on the track. But, very few people track their car. For most Mustang owners, they will spend their life with their car running through the gears and an occasional drag race on the street or at a dragway. In that case you will hate the 3.73's because you will hit the rev-limiter in 4th gear before you hit the trap at the drags and you will go through first gear so fast after installing that S/C that you will learn to hate those gears.
Put in a set of 3.55's!!! They will lower the gearing enough to be spirited with the initial mods you are planning. You will notice a massive difference in the car in terms of launch and it won't drone at highway speeds. And...when you put on that S/C you will have a big smile knowing that you took the right path at the get go!
I have a 2015 with countless mods (see Building a Super Snake
Clone posts), and have settled on 3.55 gears with a 2.9L Whipple S/C. Eventually (next year) it will have Methanol injection. I love the 3.55's. I have an authentic Super Snake (2.9L Whipple S/C with 3.73's)....it is great at a road course but I really dislike the 3.73 gears while driving around on the street and I end up topping out speed-wise in 4th gear about 200 feet before the trap at the drags...which is very frustrating.