Congrats!! You bought a great car. I have a 12 Boss there are some must do mods. There is a good chance some or all of these have been done already, so check before you start ordering parts. The big one is the clutch. If you still have the factory clutch then it has to go. Boss 302s suffer from what is called high rom lock out. The stock clutch which in the same as the Mustang GT clutch cannot handle the higher readline. There is a nylon bushing surrounding the cluth disc splines which flex above 7000rpm causing the clutch to partially reengage preventing you from shifting. Any good aftermarket clutch will correct this, most guys also go with a lightended steel flywheel . If you can shift above 7000rpm then the clutch has already been changed. If not, since the trans is out also get a steel braided clutch line and replace the stock shifter with an MGW Race spec or Barton Hybrid III and replace the fluid with BG Syncroshift II fluid., which should be done even if you dont replace the clutch. Many of us have replaced the two piece driveshaft with an aluminum 1 piece, recommend but not necessary. Boss Mustangs have the same axle hop issues as other S197 mustangs any good aftermarket rear arms correct that. Many of us have lowered our cars, both Ford Performace and Steeda make Boss specific springs. But really its up to you. The Boss engine has forged internals so they stand up well to forced induction. If you plan on tracking the car than you could think about upgrading the brakes, coil overs and a watts linkage but there are plenty of guys who track them as is. its.
Its totaly up to you.