Mostly good suggestion but there's always room for improvement.

Wheels: XTs are excellent an excellent choice for a hub if you can't afford Phils. LX would be just about as good at much less cost. I couldn't suggest one rim over another, however. I have a set of Ritchey OC rims but they don't make them in 36 spokes anymore...pity. It was a really good idea for reducing dish.

For spokes, there's only one real choice. DT Alpines. Thicker, stronger elbow for a beefier wheel without too much of a weight penalty.

Headset: Threadless if you can. Simpler to adjust and maintain. Very field serviceable, unlike threaded headsets.

Stem: Again, threadless. Just about any threadless stem is stiffer and resists bending better than a quill.

Tires: I tried the Panaracers and hated them. They seemed tall and squirmy. Continental Contacts are pretty good.

Crank: The Sugino is okay but, if you can afford it, a Shimano Trekking with external bearings is the way to go. Dead simple to install and maintain. If you want less expensive, Jenson sells a Deore with 48/36/26 in an Octalink bottom bracket for the same price as the Sugino. The Octalink can be used with integral crank extractors while the Sugino can't. The Shimano cranks will also take much smaller inner rings...down to a 22.

Seat post: The Salsa Shaft is good with the tilt decoupled from the fore-aft adjustment. But the RaceFace seatposts work a bit better.

Front derailer: Best triple for road use (it will work with any crank from a 52/42/30 105 to a RaceFace Turbine to a Shimano XT trekking) is the Shimano Tiagra. Very, very forgiving. Wide between the plates and the plates themselves are narrow. Less fiddling to get it to stop rubbing then an Ultegra. And it will work with STI.

Bags: Bags with lots of pockets have a couple of problems. Either the pockets don't get used and are useless or the pockets get used and encourage you to carry too much unnecessary junk. Ortlieb Rollers are just a big single pocket that are waterproof and attach to the bike without hassle. I use ziplocks to organize my stuff in the bag but I'd do that anyway

And I wouldn't carry a seat bag. That's prime real estate back there. It's too handy to pile bulky lightweight stuff back there. For cameras and other stuff you need while you ride, it's hard to beat a handlebar bag. Put a camera in a seat bag and you'd beat it to pieces