Pain during exercise

I am a college Ultimate player at NCSU. I'm in my winter workout schedule trying to get ready for the spring. I feel like I've been making good progress lately, except for a couple setbacks. During my long runs lately I have been having problems with my shoulder and knee. The knee is a dull pain that I think is being caused by doing lunges during my circuit training days. I figured this out while doing my lunges when my knees were both bothering me a good bit. They stopped hurting after I stopped doing the lunges. I switched the lunge part of the circuit to rocket jumps instead for today.

What other exercises can I do that are similar to lunges but won't hurt my knees as much? Or is it possible that I am doing my lunges wrong and this is what is hurting my knees? When I was taught to do lunges I was taught not to let my knee touch the ground but to get it as close as possible. The pain occurs when I am at the bottom of the lunge, and it comes from the top of my knee in the middle.

The other problem that I've been having is shoulder pain during my circuits and to a lesser extent during my long runs. The pain is very sharp and very intense. It makes it so that in order to keep running I have to do it with my right arm by my side. It only occurs in my right shoulder. It becomes the most apparent during/after my circuit training. Mostly towards the end of the training when it starts to get hard. My circuits involve push-ups but it doesn't feel like a muscle pain. It is more like a nerve pain to me. It subsides as soon as I rest for about 5 minutes, and is usually gone once I finish my stretches. It is so intense that it makes it difficult to even do my cool-down run after my circuits.

What is causing this shoulder pain and how can I get rid of it?

Any ideas are welcome.

Thanks.
 
As for the knees, sorry, I can't help you as I, fortunately, never have knee pains even after a serious ACL injury in 1984.

As for the shoulder pain, I am experiencing that right now. I have been diagnosed with shoulder tendinitis. Do a google search for this and see how these symptoms compare? Then, I would recommend you go to the Infirmary and see what they have to say, although the quality of care at university infirmaries is low, but at least it's free or at least used to be.
 
Knees are a tough one... I suffer from a myriad of knee maladies... mostly cmp in my right knee that will eventually require kneecap replacement.

There really aren't many exercises like lunges that you will be able to perform that will reduce pain. I recommend continuing lunges and squats but reducing the range of motion... instead of a full knee bend (90 degrees) limit yourself to a 30-40 degree bend. And definitely stay away from leg curl/extension machines, as they cause your kneecap to grind excessively in it's joint glidepath.
 
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