It all depends on how the transmission is mounted. If the transmission is solidly mounted, then rubber mounts on the engine ( or anything that allows the engine to rock even slightly) will be a death nail to the transmission case.
Solid mounts will transmit an enormous amount of harmonics to the chassis. Vibrations from the engine will be felt.
A larger diameter exhaust is noisier, the lack of a sound deadening barrier between the firewall, and floor will allow noise, and heat to transfer into the interior. Carpet and padding will help, but not be as effective as if there were a "dynamat" like material installed first.
But all of this is mute if what is under your car for an exhaust is typical for most mustangs...
The typical hack mod is to get rid of the cats, and throw on a set of flow masters. Losing the cats increases the tailpipe emissions, and creates the infamous " I smell like exhaust when I drive/ ride in my car" syndrome.
The flow master muffler is just a noisy ass metal box w/ a couple of diverters welded inside.
Reinstall the cats, get an alternative aftermarket muffler. That alone will lower the noise level more than anything else you can do......the power gain from a flow master muffler over a quieter muffler is soo minimal,..it's not worth yelling at each other just to go for a drive, or smelling like a tail pipe when you do.