While my time on trail and mileage are roughly similar to yours, my elevation gain and loss, and elevation levels, are much lower.

I've always had similar issues with packs; after a couple of hours, they seem to have slipped a bit and are bearing funny, and at the end of the morning, or the day, it's nice to take it off for a bit. I'll sometimes experience mild "saddle sores" nowaday, and I find that the Thermarest and even NeoAir don't completely stop my hips from waking me up at night. (But that usually happens once or twice a night at home, too.)

The last year, I've noticed some pain in my knees, too. They'll become a little "ouchy" by noon, but then never get any worse. I've also noticed I become winded a bit easier than I used to.

And this mild deterioration had set in despite conscious efforts to carry less. I did find out, on my last hike, that I really don't have an option I thought I had. I had winnowed my gear down to two sets, equivalent in function but not in weight and convenience - and I thought my choice was going to end up made on the basis of convenience. The last trip, with a starting load of 32 pounds (which included 4 pounds of water, and would have been only 27 pounds with the lighter gear), has convinced me that I really need to choose based on weight. I found myself getting winded more quickly, and found my hips somewhat more sore at the end of the day. My knee was no longer "chatting" with me - it was carrying on a rather insistent conversation. I also am finding that I am not quite as agile as I once was. Stream crossings that once found me hopping rock to rock now find me stepping deliberately, placing my poles. I also find I'm not as graceful getting into and out of my chair kit - and that the chair is no longer a luxury!

Part of this may have been a matter of not quite being back in shape after a less than active winter, and part may have been a matter of trying to keep up with the 2.5 mph pace the younger folks were setting. But some of the soreness and lessened agility is age.

So, while it's no comfort, and won't stop either of us from continuing to backpack, you're not alone.