When I first got my XR600, I geared it down to 14/52, but didn't like it because I was constantly shifting. I went back to the stock 14/48 combo, and it worked a lot better. I don't think its too high for any trail, because you've always got 1st, which still will putt along pretty slow.
And yes, its always best to replace the chain and sprockets all at once. I believe the 600 comes stock with a 110 pin chain. It isn't difficult at all to replace the rear sprocket, just pull the wheel off and unbolt the sprocket. Master links on O-Ring chains can be sort of tricky. If you're gonna take it to a shop, I'd guess it shouldn't cost any more than an hours worth of labor at the most.
As far as your exhaust, I wouldn't try to make the Supertrapp any quieter. No matter how many discs you take out, it'll still be loud. And if you take too many discs out, then you start hurting performance. If you want quiet, without being too choked off, consider trying to find a used stock exhaust, and use something like a White Bros. Vortip or Thumper Racing Stealth insert. Big Gun also sells a quiet core muffler, and FMF just came out with the Power Core IV Q, which is supposed to be pretty quiet.