I'm late to the game, but here are some observations/suggestions:
1) You know a good bike shop when you walk in. Might not be the snazziest, but the real bike shops don't sell what they need to push. They sell what will work for you. They love to talk bikes. Just get them talking, push them for info, if they can't get past "well this is our best bike because" I'd move on. Ask them what they think about components for your level of cycling. If they say, "Dura Ace" without asking about your price points and objectives, walk on. If they don't know what Dura Ace is, or why it's so good, walk on.
2) I second Felt! I've had two. Relaxed-fit bikes with good racing street cred. He is into the bikes more than the markups, so you get a screamin' good deal at whatever level of bike you choose. I don't think I've replaced any stock Felt components -- I find their quality is very good. Nobody, except the in crowd, has heard of Felt. It ain't some generic brand, I can assure you. Moreover, the combo of relaxed geometry and race-level components works great. That being said, the Madone is a nice choice, although Trek has kinda stretched the name to cover a big range, past the original "Bike that Lance rides." Some Madones are more equal than others.
3) I started with Shimano SPD, and liked them, but once I tried Speedplay I've never looked back. Better feel, better comfort (it's really nice to have the extended play (pivot angle) of the Speedplay. I went with the X-5, and am really pleased, even though it's not the Cadillac of the line. IMHO, a big improvement over SPD. But as Scott mentioned, you don't want to walk around on them, so by all means buy the covers for them.
4) Get a bike computer that has a cadence sensor and heartrate sensor. You can separate the two, but it's great to have all that info in front of you. If you don't know your heartrate, you have no idea how hard you're working (and it's probably too hard on hills).
5) A century is a long looooooong ride. Your azz will be sore. Make sure you use chamois cream before the ride (hint, it goes on the chamois, not on you).
6) Enjoy -- cycling is great fun.