I've seen very fit and able people struggle on trail (I run a hiking group). Part of the issue is elevation, sometimes, and just the endurance and conditioning of the body to the stressors it's subjected to. Your feet are getting long periods of friction and extra weight of the pack put on them, your joints too, and your lungs aren't yet ready for sustained uphill climbing.

Hiking is about the best thing to prepare you - put on a pack and hike, short distances at first, increasing as you gain stamina. I can do a 15 mile day - I'm not going to go 4 mph, but I can plod forever without stopping, without pain and suffering after the trip. The goal is to hike at a pace you can sustain. Plan breaks at regular intervals for food and water tho. The other key - learning how much more water you need and to snack more. Drinking enough water during the day for the level of activity you are putting forth will help reduce post trip soreness.

Find a hiking group and go with them regularly. That'll help a lot.