Ask them if they charge extra to swap out components. Usually, they shouldn't, if you are spec'ing a comparable quality part. They may have you pay the difference for upgrading parts. Also, in fitting you to the bike (another question - they will do it, won't they?), will they swap out the stem for one of proper length/rise for you?
As about service for the bike - most shops request that you bring the bike back after X hours of riding for a tune-up. Talk to the folks in their service department. If you are comfortable with the shop and the folks in the service department, you're more inclined to come back.
Remember, when you buy a bike from your LBS, you are (hopefully!) creating a relationship with a shop, not just buying an object to toss in the garage and forget about.