1. gas. Get ceramic logs. We did it this year and man that fireplace is hotter than anything wood could produce. Plus you don't have to mess with cutting wood, storing it, having Black Widows nest in it outside, etc. Best thing I ever did in home improvement.
2. Solid wood cabinets. They'll last and cheap stuff will wear out badly. Pulls are completely aesthetic.
3. Gas/think about convection burners as well. Microwave in wall is good but could be problems re-mounting replacement if not exact dimensions.
4. Not a big concern.. too much prewiring = "we shouldn't done that...." later on IMHO.
5. Steel wears better than brass. Other than that, completely aesthetic.
6. We're tossing wood and vinyl and going for staining the concrete, and area rugs. Wood eventually yellows and despite what their manufacturers claim, so does just about everything else resembling wood. Concrete keeps house much cooler in summer, easy to warm w/rugs in winter. Only caveat: little kids under 2 might be a hazard if they fall.
7. We just put in triple-paned EnergyOne Windows. Not cheap ($14K) but they do an amazing, no amazing job of keeping house warm (winter) and cool (summer). Our windows are lifetime warranty so I don't much care what the material is, but I think it's a composite vinyl. The glass is >>> important than the framing IMHO. Pella/Andersen, etc. not much bang for the buck.
Addenda: 1. Low hearth in fireplace. It makes the room look and feel bigger and I never liked those "sit on a ledge" type hearths. Ours is only 1 brick high but it's nice. 2. Moulding at least 2" on bottom, it looks nice. Ceiling - meh, up to you, never thought it added much.
3. Propane - 1,000 gal tank? Are you preparing for the next Ice Age? How big is your house? We have a 250 and only fill it about 2X per year. I guess you could have that huge mother buried in the yard but man that's a lot for a house that's not a brothel. I can't imagine a scenario, unless last Feb. 12th-19th runs all winter next year, that you're going to need a tank that big. But if you want it and can afford it, no harm done. 4. Double - no, triple - planned storage space. I mean it. Really. It's far too little, trust me. 5. Likewise, make garage bigger than you'd think. I'd tack on 6' to all sides if you can spare the $. It's very easy to underestimate the dimensions for this.