A couple of other thoughts on your pain.
The pains may just be due to the fact that you have increased your riding a lot in a relatively short time. That means new stresses on connective tissue regardless of how good your fit is, and those tissues may just need time to recover before being stressed again. Easing off on the long/hard rides for a few weeks may fix things.
A couple of other thoughts on the knees--and there can be MANY different fit and technique-related causes of knee pain, so these may not apply to you.
1)
Pushing in too high a gear can cause knee pain - so consider lower gear, higher cadence if that may apply. People usually rec 80-100 revolutions per min.
2) Iliotibial (IT) band syndrome - usually on the outside of the knees over the bony prominences. I got this from having the
seat too high (or too far back can do the same thing) which makes the leg too straight on the down stroke. See
this video. You can also do stretches or use a roller to help with that--rolling on the outside of the thighs.
3)
Seat too low can also cause knee pain, especially if pushing hard, climbing hills. It's kind of like doing squats and transfers a lot of force across the knee.
4) Pedal to shoe attachment and knee alignment--if you are clipped in, having a system that allows more float may allow a more natural knee alignment. Adjusting the cleat position can make a big difference depending on the system you use, or selecting a system that allows more float.
Shoulder pain is frustrating. That has been my biggest complaing on a few of my long rides. I have played a bit with stem length/reach and such without obvious help. It still crops up know and then, usually when I increase my riding time quickly.