Look, the #1 thing when buying a bike is that you get a frame with the right size and fit. All of this other stuff is relatively irrelevant compared to fit.

For tire size, anywhere between 23c-28c is the fastest. I'd just stick with what came with the bike (what's important is to get a skinny slick if you want to be fast, anything knobby will slow you down with no benefit since you're biking on pavement, anything wider will make you a little slower but perhaps be a little more comfortable - but 25c has been comfortable enough for most people).

If you have a price point, they're all basically going to come out at around the same component group level. Here's a breakdown:
Sora/Tiagra - In their modern versions either is a solid groupset. Not as "polished" as more expensive groups but functionally not much different. It's like buying a Toyota Corolla.
105 - More expensive, a little smoother. Might last longer.
Ultegra - The smoothest (and might last longer), but it's expensive, but most of that cost goes into feel. It's like buying a bmw - in some ways it's cooler, but functionally it does exactly the same thing as the less expensive version.
Dura-Ave - You pay a lot more money for it being somewhat lighter weight. Not worth it for anyone but racers, imo.

Frame: Alloy usually means aluminium so those are usually the same. I like full carbon myself, the ride is smoother on models designed for that, imo for commuting I'd rather have a good full carbon frame than have a cheaper frame with more expensive components.

You can buy a full carbon 2014 Specialized Roubaix for $1725 -
Specialized 2014 Roubaix Base Road Race Bike

Or the 105 version of the same bike for $2,025 (though this is getting a bit above your budget) -
Specialized 2014 Roubaix Sport Road Race Bike

I prefer a carbon front fork, no matter what other frame material is used, because it's usually a little nicer on the hands. But almost all road bikes come with a carbon front fork now.

You could also go the other way - only spend $800-$900 on a aluminum/steel bike and see if you stick with it.

Again though, really, bike size and fit are going to make more of a difference to your riding than any of these other factors.

Of these bikes that you mentioned:
caad10 5
fuji roubaix 1.1
Giant Defy 1

I would go with either the Fuji Roubaix or the Giant Defy. Doesn't matter which one. The caad is designed for racing, which in an aluminium frame means it probably has a harsher ride than the other two, both of which are "endurance" style bikes more designed for a smoother ride. (To be clear, they'll be equally fast in speed, the difference is whether your handling is razor-tight or not - I personally prefer more relaxed handling as it's not as fatiguing to keep track of.)

Though as I said, I would personally prefer the Specialized Roubaix Base at $1,725 for it's full carbon, relaxed geometry frame, if it was me.

P.S. You know, don't let yourself get to overwhelmed here. Everything in the $800-$2000 price range is decent bikes. You'll most likely be happy with anything you get in that price range, as long as you get the right size and fit.

P.P.S. I think rack mounts are nice, but if you're not riding in the rain or right after the rain fenders are not nearly the big deal that other posters have made them out to be. Fenders are important if you're a "ride all the time in the rain" kind of commuter, not so much if you're only a fair weather commuter.