Yep, I agree, find a good shop... typically, the national chains don't have the personnel with the skills to do a good custom exhaust.
I recommend going to a good local shop and talking them through what you want to do, going so far as to get it on the lift with the guy who is going to do the work and walking through it. I also recommend having them build it with flanges in key places, like the cat and the muffler. The Magnaflow Hushpower muffler is low profile and has a good sound: quiet at speed, throuty on acceleration and burbbles like a V8 when decelerating. It is a little on the expensive side, but is stainless and will last a long time.
The other advantage to a local shop is that you can have your exhaust routed anyway you like. I had mine run inside the frame rail from the down pipe (I a have 1981 FJ40 with headers, but same difference) then across the tub from driver to passenger side in front of the rear shocks and then out the passenger side behind the rear wheel like stock. This gave me the room to put an air tank where the original muffler was.
HTH
Good luck