Is your set-up loud? I expect it is louder than stock, but what about under load and at cruising speeds? Any Drone from the aftermarket exhaust?
Also - what gains can I expect (HP and Torque) with a DP/DPF delete, stage 2 Malone Tune, while keeping the stock Cat and Muffler?
It is louder than stock but by no means is it a loud car. At cruising speed I can hear the engine more than I did when stock but I wouldn't call it a drone. The turbo acts as sort of a muffler on its own so even totally straight piped these cars don't get very loud. This is all subjective though, what I consider "not loud" other people might have a problem with, your best bet would be to try to find a car in person to listen to or check out some YouTube videos to get an idea.
Malone advertises 184bhp/333 lb/ft of torque on Stage 2 w/ dpf delete. I haven't dyno'd the car but I would believe those figures given how it drives. That's ~44hp/~100 lb/ft over stock levels. It is a completely different car after the tune, if I had to do this again I'd have tuned it the day I got the car. The torque is very, very addictive.
Stock muffler shouldn't restrict power at all, I'd imagine the stock cat would though. Those questions are probably better answered by Malone or one of his vendors, they'll have more experience with different exhaust setups than I do.