did not see any additional information. there are smarter folks than me here, but my thoughts are:
butt pain - your anatomy is unique to you and it takes a while to find a saddle that matches you and your riding style. expensive is not always better. Cushioning may feel good on short rides but really hurt on long rides. I tried six saddles before i found a couple i liked. Most Bike shops will let you take a saddle for a ride. Talk ot any riding buddies, often they have saddles you can try.
Bike shorts are a must- the chamois (padding) also varies a lot- some people like thinner, some like thicker. Get a reasonable priced pair (as a big guy I switched to bibs, never going back, even though my wife laughs at me) and use chamois butter - helps.
Bike position is important, you need to learn to rotate top of your hips forward. and to sit at the back of the saddle - I have a tendency to slide forward on the narrow part - hurts.
You need time in the saddle to "toughen" your butt - And learn to stand every ten minutes or so.
Knees - usually this is managed by seat forward and back positioning. lots of sites discuss this.
Knees can be impacted by cleat position on your shoe.
also the foot angle, if you toe out a lot - may need a "floating cleat" system
heavy pedaling can make this worse, try to increase rpms and use less mashing
Hands (and shoulders) - this is where i struggle too. Too much weight on hands - after 2 hours hands and shoulders are killing me. I raised the handlebars, that helped some - still too much. I change hand position often but still hurts , going to try to reduce stem length (bring handlebars closer to me - see if that helps. Pro bike fitter was no help on this. told me to do more situps! any one else have suggestions would love to hear them.
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