This is going to be a long one I suspect... I'll start with saying please let us know what the second opinion says about your car. As a former mechanic (we like to be called technicians these days :p ) and a former service writer for various places including Pep Boys and a couple dealerships it really doesn't matter if you're a man or women what you get charged or what we tell you needs to be done (some exceptions but VERY rare). What does change on an hourly basis is the technician's attitude. Did he just get a 6 hour job done in 3 hrs (good thing) or did he just have to put a heater core in a Ford Taurus (pain in the ass). Did his girl just give him some crap about cutting the lawn when he gets home, or possibly it's Thursday and he has only 25 hrs in for the week and he needs to make that up by Friday. Simply it comes down to the PERSON you are dealing with, not the chain (midas, pep boys, Dealerships). I now work at a job where I visit many different shops on a daily basis, some are run better then others some places have a good crew some don't. On to your specidic questions:
1. If the garage is not a "muffler shop" most places will replace the exhaust as an assembly which means if the muffler is bad they will replace it to the next joint in the exhaust. I THINK on the SEV6 that would bring you up to the resonator, possibly the cat. You said the Cat with a question mark so I don't know if they said to replace that. If they did it sounds a little funny to me. How fast it wears out is another issue in itself, short trips where the exhaust does not burn off the moisture inside will work to destroy the exhaust faster. You get enough snow in pittsburgh (and roadsalt) to have an effect on the exhaust.
2. The brake prices sound high but for the rears I'm betting they are including new calipers, I dunno if you need them. For the fronts that's not completely out of line especially if this is a dealership and if it's not they are probably including new rotors in the price.
That's my thoughts on the subject. Try to find a couple garages that are convenient to you try them out when you have the need. See who seems to treat you the best. It is true a nicer looking shop is usually a better place to go although sometimes slightly more expensive. If you were on this end of the state I'd offer to check it out for you. Good Luck!
