Hey guys, today I sat down to practice Picking. I started working on some 3nps scales, and noticed that when I was going up and down, my right shoulder area, really close to my neck, was experiencing some serious tension. It eventually started to ache, and I quit, due to not wanting to injure my self. Any ideas what's going on?
Chances are, you're WAY too tense. Try using your wrist to pick, and use a loose wrist.
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Chances are, you're WAY too tense. Try using your wrist to pick, and use a loose wrist.

I do. My wrist is completely relaxed when I do this. I think it might be from me trying to make my string transitions too small.
Use your bicep to move up and down. Try to do it very slow without picking anything, just move your arm from top to bottom string and back (while holding a pick) very slowly (count to 20) and pay attention to what is happening to your muscles, you will get a hang of it quick, just remeber that bicep is the muscles you should use, not your shoulder, back etc..
Good forearm strenght helps a lot too (it's all connected)
Yeah, this is sympathetic tension. First check that you aren't tensing your shoulder because of your posture. Then work on playing those scales but focus on your shoulder - try and keep it loose throughout. If it's any comfort almost every guitarist struggles with this whether they realise it or not.
Also, you might try one more thing.

Grab your guitar and a pick and grip your pick as hard as possible, you need to feel tension in your forearm and a little bit in bicep, but not in your shoulder. If you get tense in your shoulder, then try to "move" that tension to your forearm. Keep it like that for 30 seconds then rapidly release, but don't drop they pick.

If you are into fast alt picking you have to have a bit of tension in your forearm, otherwise you won't be able to pick fast and clean at the same time (pick will get away from the strings, because your forearm will react to wrist motion and drag it away (inertia)), but it's more like a burn than anything else. Shoulders should stay relatively relaxed.
TBH, I believe that most tension problems are either mental (playing too hard things) or caused by lack of bicep/forearm strength (which you need to play guitar, not very well known fact ).