Hi. I'm located in Washington D.C area and need a setup pretty badly. Haven't gotten one since I got my guitar (PRS McCarty Standard) about 5 years ago.

The intonation is pretty bad, and I've read that you need truss rod adjustments with higher gauge strings (got 11's, not sure if that would be a problem though) which I've been using for a while.

The guitar isn't in perfect condition, but I'm just worried if anything happens to it. Like a scratch, dent, or if its stolen. Am I just being paranoid?

Also, it's $55 for intonation, action adjustment, truss rod adjustments, cleaning, and fret polishing. Is this a good price?
It's a bit high, but a setup doesn't always include fret polishing.

If you're really worried, you can do it yourself. Intonation and truss rod adjustment are skills every guitarist should know. They're not difficult. Take a look at the setup sticky in EG.

The thing to ask at the shop is if they have a luthier in-house or if they send the guitars out. If the luthier is there on staff, you really shouldn't have any problems. Some shops collect guitars in need of service, tag them, and send them out to a luthier at the end of each day. You'll probably want to avoid that. I think talking directly to the person who's going to work on your guitar will do a lot to make you feel comfortable with the process. A setup is really basic, I don't imagine anything will happen to your guitar.
Sounds cheap. It runs around $80-100 in my rather large and musically diverse city.

You can pretty much do it all yourself. Don't worry about scratches and dents, instruments are meant to be played.
Scratches and dents....... They're called character!

As the others said, I wouldn't worry about the shop "treating your guitar bad"

Before taking it in, try it your self, whats the worst that can happen? You plan on taking it in for a set up anyway, may as well do some reading and giving it a try yourself. Being able to "work" on your guitar really is an invaluable skill.
f your penis keeps dipping in the toilet water........just toss it over your right shoulder...
Thanks guys! I have a Boss TU-2 which will hopefully help with the intonation (although it doesn't have the really fine markings of say the TU-3).

As for the truss-rod adjustment, I've heard it's not really a big issue, so I'm not gonna worry about that. Seeing as I only need to fix the intonation, set-up for $55 might not be worth it

As for scratches and dents, don't mind the nick on the body by the input that I created, and other dents, but wouldn't want some stranger making more!!