I was going to just post when it’s all done, but I better start posting or I’ll forget some stuff. Here are some parts I have now, costs, and what I’ve learned about them.

Frame and fork: Surly Cross Check 60cm black. (Yes, another black bike. Well, it was black or this awful green.) $480 shipped.
It’s a “cyclocross” frame, which means it’s for people who do this crazy cyclocross racing, I guess; whatever. A little more durable than a road frame. If a road bike is 1 and a mountain bike is 5, and your hybrid is a 3, cyclocross seems like 2. So that’s nice for me: I’m going over crazy Pittsburgh potholes daily, and would love to take it touring someday.
As for the specifics, Surly seems to be making bikes in the range I’m interested in: nicer than the bike shop entry level stuff, but not race/pro/hardcore quality. I think they’re a good brand to consider if your budget is around $1000. That probably seems like a ton of money for a bike to people reading this, and yes, it is. But it’s all relative.
Others I was considering include the Surly Pacer (more of a road bike), the Soma Double Cross (very similar to the Surly), Soma Smoothie (more roady), Velo Orange Pass Hunter (maybe an extra hundred bucks, and more touring-ish), and the Pake C’Mute (kind of a step down, and hard to find).
I got it faced and chased, as Surly recommends, for $40. Not sure if it’s super necessary.

Wheels: double-walled wheels from Iron City Bikes. 700c x 28-38. 32 and 36 spokes. I don’t know much about the hubs. They do have disc brake mounts, which is useless to me, but they were the ones that they had on hand. Quick release spindles, which maybe is not awesome. $144 for both.
Rim strips: there are some that you have to glue, and some that are stretchy. I got the stretchy ones. Not sure why you’d want the gluey ones. $7*2=$14.
Tubes: stock tubes for 700x25-32. Like $5 each.
Tires: Vittoria Randonneur 700x28 tires. (note that the wheels and tubes are both a range. I wanted 28-width tires and then bought the wheels and tubes to match. 20-25 are kind of road widths, so 28 is kind of the first step up into something a little more durable and softer, but still pretty light and quick. Good for touring.) They are supposedly pretty puncture resistant. $40*2 = $80. Got these from Top Gear Bikes. They’re good folks too, have been helpful. I think they’re a little higher than my price range in general; that $1000 is a small amount of money to them. But they’re nice.

Headset: Cane Creek 40 Series 1-1/8" External Cup Threadless Straight 34mm Black EC34/28. $43. This is the part that connects the fork to the frame so you can turn smoothly. Cane Creek is a reliable brand, as far as I can tell; folks recommended it to me. But I don’t think it’s super critical; others work fine too. The only other brand I heard people talking about was Chris King, but those are crazy expensive and don’t work any better.
Steer tube spacers: a handful of them, for $10. The weird thing about forks is that they always come longer than you want, so you have to saw the top off. Saw off! A part of my bike! Needless to say, I was terrified of cutting it too short, so I just got a bunch of spacers, more than I can possibly need, so I can try it as is, and then remove spacers and recut if I want it shorter.
Stem: at Kraynick’s, they’re all $20. Just got a regular threadless one. (I was toying with getting an adjustable one, but you don’t see them around, and I think that’s because they’re just one more thing that can break, and they probably make it less stiff. Stiffness is good.)

Cranks: Shimano Sora FC-3550 2x9 Road Crankset 50/34T 175mm Black. That’s the parts that the pedals attach to. The big choices here are: 2 or 3 front gears, and how many teeth? I picked 2, because it seemed easier. Then I picked 50 and 34 teeth, because those seem on the higher end, and I tend to pedal hard, rather than fast. (I’ve heard this is not a great thing. I guess I’ll work on that someday.) Oh, also, decide whether you want square taper, splined, or two-piece. Two-piece is the future, I guess. It means you can have external bearings, which means that they last longer and do better. Okay. $60.
Bottom Bracket: Shimano 105 bracket. 105 is a step up from Tiagra, which is a step up from Sora, but whatever, they had it in stock at Top Gear and it was only $4 more. $30 total.

Okay, that’s all I’ve got so far! Pictures will follow at some point. I’m thinking of calling this Stephen Malkmus, because hipsters respect it and it’s best on Pavement. We’ll see.