My last section hike on the Long Trail, 7 days, had rain all but one day. Wet feet are what you get. Forget about any fairy tale Goretex this, Sympatex that. The wet gets onto your legs and into your boots (or trail runners if you're me). Back then I WAS using heavy boots (Limmers), and I regret that I hadn't considered footwear that would drain and not stretch. Nylon strapping with nylon breathable fabric is what makes a good wet weather shoe or boot.
Upper body: If it's not too cold, just wear your polypro (poly-whatever) or wool, and be thankful that you're being cleansed as you walk. In temps. below 60, I recommend a poncho. If it's windy, tie a cord around the waist or hoist the back corners up and tuck them into the front of your pack belt.
Any way you look at it, you'll get wet.
I've found that, for the feet, a little rubbing alcohol toughens up the soft skin caused by constant exposure to dampness (and kills bacteria, etc. that can cause infection).
Don't use it on the "personal areas", however, as it will burn like heck.
Thigh chafing is something I deal with on most long hikes.
There are sports lubricants which work well for that area. Wiping with a baby wipe helps immensely in "that" area.