I've seen that the #1 problem of backpackers on our Sierra Club trips is sore &/or blistered feet. Often I'm "Dr. Goodfoot" when it comes to serious blisters B/C I carry the community 1st aid kit & have Outdoor Emergency Care training (ski patroller).
The two best things for prevention of these problems are:
1. comfortable shoes or boots that are broken in and have good footbeds
2. well conditioned feet that have toughened soles from miles and miles of walking
A custom fit footbed (insole) seems to help most of all when conditioning feet. If anything it reduces the amount of foot conditioning needed by 1/4.
And the #2 complaint seemd to be sore shoulders. All I can say is be sure to carry a daypack of about 15 lbs. on conditioning hikes. A good 10 mile hike is necessary once a week for several weeks before the backpacking trip of 5 to 8 days. Plus a few 5 mile hikes during the week also help a lot to maintain foot sole toughness.