I have been doing Chin-ups and Pull-ups for many years and have never experienced shoulder problems due to these movements. Naturally, we are all different. However, there are two movements which I will not do because I have found through watching others and general experience (never read a study on it sorry) that they will harm your shoulders. You mentioned them both!
Wide grip Pull-ups
Behind the neck Pull-ups
Heal your shoulders first. After they are feeling better resume the Pull-up, Chin-up training but remove wide grip and behind the neck. I bet you won't have anymore shoulder problems. Give it a try and let me know what happens.
First of all I am amazed at the amount of people who continue to perform a movement when they feel pain while doing it. It matters not that your cousin Fred can do this particular movement every day without pain. If the movement bothers you stop doing it! All you are doing is causing damage.
A couple of years ago I posted something about the "evils of Bench Pressing." However, that only applies to those who do not have a mechanical advantage for it. Those who have long arms and a shallow chest are more likely to have shoulder problems from Bench Pressing than those with short arms and a barrel chest. I don't have any studies to prove it. All I know is that over a period of 30+ years I have seen shoulder impingment injuries directly related to Bench Pressing. The funny thing is that the overwhelming majority of these injuries were on those with longer arms and a shallow chest!
Some people had the audacity to post back to me saying that they had long arms and a shallow chest and never had any pain. Most of these people had not been lifting long enough to even worry about it. I am talking about long term injuries!
I think we have to accept that there are mechanical differences between people.
Why is it that those with long legs have a more difficult time Squatting? Just as those with longer arms have an advantage when it comes to performing the Deadlift.
We are all ready to accept these more obvious mechanical advantages and disadvantages. However, when it comes to the more subtle mechanics no one wants to accept a limitation.
Stop doing wide grip Pull-ups! I have seen many over the years absolutley wreck their shoulder doing these over a period of years. Yes, I know some people can do them with no problem. However, you are not one of those people. Accept it and move on!
As to you specific question. I first recommend the following:
stop doing any movement which causes pain. Your body is talking to you and it's telling you that what you are doing is hurting it. The damage will grow worse as you get older and you won't be lifting anything heavier than a Protein shake (preferably Grow!) if you keep it up!
Use Ice/Heat therapy. It's basic, cheap and it works as well as Ultra Sound and the other magical machines that are available.
Go to a good Chiropractor. Mine has been worth his weight in gold through the years.
Go to a good message therapist. Also an ART' practioner may also be able to help you. Ask around to see who is the best in your area.
Finally, I want to recommend a device which has helped me stay in the game many years after my friends are on their sofas holding a can of Budwieser. It's called the "Shoulder Horn." Here is one place where you can pick one up: