Wheel size- 23s or 25s will serve you well. Just get good quality tires (gatorskins), in the rear at least.
Pedals- for my build I was limited to pedals that had a 1/2" spindle, so i've got cheapie ones w/ cages now. Will order some better ones once my funds increase.
Water Bottle Cages- Yeah...It's the cool factor. My stickered-out nalgene goes everywhere i go, so it stays on the backpack. No need for cages, but it also looks cleaner.