I have a 40 series flowmaster on my 3 and it sounds great nothing like your typical 4 cyl with exhaust. very deep tone from 1k to 4.5k then it is a little raspy
Sounds like someone has no idea how to use a buffer. Next time try a piece of 2000 wet dry paper use it wet, sand scratch lightly, then buff with some 3m perfect it III compound. If the scratch is still there then I would suggest painting.
Factory hood will be about $400-500, plus paint which would have to include blending the fenders or else the paint will not match. unless it is black then this will not be necessary. paint approx $400.00
I eliminated the resonator and installed new 2.5" pipe with a 40 series flowmaster muffler and got a nice deep sound. However I do get a high pitched sound at 5000 rpm in 1st gear.