As was stated earlier on the stock converter you're not going to get much better than what you've done. My car picked up half a second in the quarter mile after my Circle D converter went in. Oh and with 3.15's.
I had many Mustangs over the course of 30 years and I'm on my second Challenger with the 392. The Challenger is more roomy and better looking in my opinion over the current Mustang. The 392 puts out a lot of torque but won't be as fast. But it's a better overall cruiser in my opinion.
You won't gain any power by replacing the mufflers and my car was slower with the JLT Intake due to the heat soak. A good tune with E85 is a real difference maker.
Impossible. JLT only sells tune required CAI. Also the longtubes need to be addressed in a tune due to the cats moving further downstream. Your car had to have been tuned before you bought it.