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Jeff Silva wrote about choosing a good repainting / body shop
The parts you should have the body shop remove are the front windshield and rear window. This way there's no paint lines next to the moulding going around the window. A good body shop will require the windows to be removed as part of the warranty that you're given.
Sanding the car down to bare metal is nice, but not required. Good body shops now use a chemical stripper that eats the paint right off of the car, but leaves the undercoating(supposedly). The only parts that would need to be sanded to bare metal are the hood, roof, and trunk. These are the panels that are most likely to peel later on, and if you get a warranty that covers this the body shop will do everything they can so that it won't peel.
If you're going to paint the car a different color, then be prepared to remove the engine, all parts from the engine compartment, entire interior, entire trunk, and a lot of other parts. Unless you just want to paint the areas that are seen. Then you don't have to worry too much. A good body shop can work around certain things to make the car look good.
If you need a bumper or front faschia painted, always remove the mouldings and trim off of it. What the body shop will do is pull them off and bend the hell out of them. Instead of reading the FSM or other manual on the proper way to remove the item, they'll just pull and tug at it until it breaks, comes loose, or bends to show where a screw or nut might be.
The only type of body shop that will spend the time to remove all of the mouldings and trim and put them away in a nice orderly fashion would be a custom body shop. These shops will totally take apart your car, rebuild it, and re-paint it whatever color you want. They'll do custom work like graphics, pin stripping, metal flake, sparkle flake, or candy. These places will charge around $7000-$8000 for a custom job and about $3000 for a basic paint job. Then the wait is about 6-8 months.
If you're in the market for a new paint job and are looking for a body shop, here are a few things to look for:
You need to show that you are very concerned with how your car is going to turn out. As soon as I told them my car was going to be a show car, they wanted to help me out and said that they'd work with me to get what I wanted (they know they'll get some free advertising out of me). Be sure to tell them that you're going to show the car, or tell them you want show quality. If you're having an everyday driver car or an old clunker painted, tell them you want 'factory' finish.
Hope this helps. It's what I did every time I went to a body shop for a quote.
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