it seems like a small gesture for a shop to swap a stem for a new customer buying a new bike at full retail, especially if they are a new shop. The shop I frequent swapped a stem at no charge for me after I had it for over a year. They kept it and use it as a swap for their rental bikes. The shop in question seems like it is being a bit short-sighted to me. As far as the OP being a PITA, it sure doesn't sound like he is. Trying to get the best deal, especially if it means getting the proper fit, is not unreasonable at all. I have seen it said thousands of times in here (and have said it myself) that if the bike does not fit properly, the rider will not enjoy riding it and therefore not ride it....The shop should just swap the stem.

Cheers,

Brian