As Arne said, we don't want to play doctor, but I've had three rotator cuff surgeries in the past four years (two on the right, one on the left), and I know a fair amount about the joint. Raising your shoulder like you were doing puts a lot of stress on your rotator cuff tendon and your supraspinatus muscle.
I don't want to get all technical, but bear with me here--I think this will clarify some things for you. The supraspinatus is a small and (usually) weak muscle which runs along the upper part of your shoulder blade. Its tendon attaches to the top of your upper armbone (humerus) right at your shoulder socket. It kind of wraps around the ball of your shoulder along the top of it. The tendon usually gets banged up at the top of the shoulder because whenever your arm comes up past 90 degrees, the tendon winds up getting pinched between the shoulder ball and your acromion, a tiny bone that extends off the end of your clavicle. (You can see all of this here:
http://drugline.org/img/term/acromion-216_2.jpg )
Problem is, if and when the tendon gets pinched enough, it starts to swell up, and that means there's even less space for the tendon to move around, increasing the likelihood that it'll get banged against the acromion again. It results in a bad cycle, and once inflammation gets in there, it can be hard to get out.
So, to bring it back to what mahantango said, when you were raising your elbow up above the plane of your shoulder, you were probably pushing that tendon into the acromion, causing it to get inflammed. Now I'm not a doctor, and if the pain is bad, I strongly recommend going to see an orthopedic surgeon, but based on what you've said, it sounds like this is what's happening.
If you want to try a home remedy for now, do this: Ice it for 20-30 minutes every night. Never heat--always ice. And take ibuprofen for the pain and inflammation. Aspirin might help with the pain, but it won't do anything for the swelling, and that's the cause of the pain here. Use Aleve or Motrin, and take at least two every morning and every evening, roughly 12 hours apart, with food and water. Now, if you have kidney issues, don't start taking NSAIDs--talk to your doctor about what he recommends before taking stuff (aspirin is hard on the stomach and liver; ibuprofen and other NSAIDs are hard on the kidneys.)
And above all, keep the elbow down so the shoulder joint is firmly in the socket. You might have to learn a new anchor point or adjust your shooting (the position of the elbow can change the height at which you're holding the bow, among other things), but it's worth it if you keep your shoulders healthy.
Hope that helps, and please see a doc if the pain continues or worsens after a week or two.
Brad