I rode 22 miles in one trip yesterday (longest single trip I’ve ever made), and 30 miles on the day. Now, my back hurts a bit, my wrists hurt a bit (handlebars), and especially the inside of my knees hurt. Is that supposed to happen? I’m particularly concerned about my knees. I’m trying to train to be able to do a century by the end of the summer, and if I’m doing something wrong, I figure I need to fix it now.
My bladder gets full.
After 20 or 30 miles non-stop my bladder starts to hurt.
Do you ride with yours knees wider than the width of your feet on the peddals? Toe in or toe out foot position on the pedals?
Pretty sure I keep my knees a little out. Probably have my toes pointed to the inside. I try to keep my toes on the pedals most of the time.
I find after a long ride that I’m sore under the chin where my helmet strap chafes 
Foot placement and knees position
I would try being careful to watch how your feet and knees are positioned. Feet not pointed out or in. Try to keep your knees directly over you feet.
Your seat being low might also add to knee trouble. For touring I like to ride with my seat higher than most would fit for a bike. Be careful not to raise your seat all at once. Some therapists recommend not increasing seat height more than 1/4 inch at a time or you could stretch tight muscles to fast.
Short cranks also require more knee strength.
Try gradually increases in distance. Some experts recommend increasing less than 15 percent per week.
In the past, I found I have more trouble with my knees if I did not regularly ride long distances. If I took four days in a row off from riding I would have trouble on the next ride if it was of any distance. But I think you are younger and may not have the problems that age brings.
Your back will get stronger and more used to riding.
Be carefull with the knees. There are so many things that can cause knee pain: muscle imbalance, low seat, high seat, short cranks, long cranks, doing too much riding without gradually building up.
Try doing some stretches and leg excercises to cross train. I found that doing squats with my feet pointed out (working the inner quad) really helped my knee pain. Cross train with a bike ride if you can as well. Make sure your seat is not too low or too high, and if you are going downhills a lot a brake will help your knees out on the descents.
Before giving specific advice it might be better to know a bit more about your ride. Was this a road ride? Mountain ride? Flat or hilly or mountainous! Your wheel size? Crank length? Is your seat adjusted to an appropriate height? What was your approximate average speed, or how long spent on each ride?
Then we’ll have more to work with.
Basic advice: Don’t overdo; work your way up to higher mileage in steps. Stay fueled and hydrated. I had to learn the hard way how important food is on long/hard rides. Listen to your body. Minor aches are normal after rides longer than what you’re used to, but if stuff doesn’t go away, don’t keep doing whatever you’re doing until you know why.
You didn’t mention your crotch. You’re doing well in that area!
Everyone else gave great advice on how to avoid having things hurt.
To answer your question, “What should hurt after a long ride”, the answer is “nothing should hurt”, provided you are in good shape.
A bunch of us did a 100km ride a few weeks ago (I was on my 24" muni). At the end of the ride I was tired, but nothing hurt. The next day I didn’t have any leg soreness. I’m in pretty decent shape right now, since I’m training for an upcoming tour.
-corbin
I tried to prop myself up a bit to stay away from the crotch pain. Already learned that lesson 
This was a ride on a bike path, with gentle hills along the way (Bakersfield, Ca). I was on a 36" Coker with 150mm cranks. The seat is adjusted as low as it can go with the handlebars on, so that if I have my heels on the pedals, I can barely reach them at the low point. I averaged ~9.5 mph overall, but I slowed down for the last 5 mi or so. I rode 10 miles in about an hour and took a 5-10 minute break, then I rode the other 12 miles in about an hour and a half, maybe a little longer. I dismounted once when I dropped my glasses, but I didn’t stop longer than it took to pick them up and mount again. After that I got dinner and rode out the remainder of the distance.
For 100 mi/160 km rides, how long do you go before taking a break? Is it better to do 5 mile increments, or is it better to do 20 mile increments, or something else? I plan to do 30 miles this weekend. How should I break that up?
I appreciate the help!