Steve - If you're getting a Specialized, see if they're a BG Fit shop (Specialized's proprietary fit program). The shop will probably do a basic fit as part of the bike purchase; you might get a discount off the price of a more involved fit. If so, it's money well spent. As for the stem, it's common for a shop to swap out stems as needed - they usually have a box full of them.

Around here, an involved fit costs ~$250. Some cyclists (not me) pay more than that for a jersey. That's what I paid, and it's the most cost-effective investment I've made in cycling.