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Hmmm, that's an interesting question. I've been in massage therapy school since last October (year ago) and I graduate in March, a CMT. I have some guesses about what might be going on, but would like to know more.
Can you be more specific about where it hurts and which movement bothers it most?
Here's what I think: your arm engages in a repetitive movement while you run - you probably irritated something in the shoulder during the event. Possibly with the adrenaline of the event forced the movement more than during training?
The advice of my instructors is that you can't go too far wrong with icing. It will help reduce the inflammation and interrupt the pain cycle that makes the surrounding muscle tense up even more. A handy do-it-yourself gel pack is to mix four parts water to one part rubbing alcohol in a reclosable freezer bag. It doesn't quite freeze solid and will conform to wherever you put it.
Pain and swelling that doesn't subside after 24-48 hours really ought to be seen by your favorite medical professional. There's a lot that goes on in the shoulder. It's not as stable a joint as the hip - the hip bones and muscles really fit and bind together, but the hip is not nearly as mobile as the shoulder. It's a trade-off: shoulder is more mobile but has less stability. What mostly holds the shoulder in place are the four rotator cuff muscles (and various ligaments). They more or less surround your shoulder blades and have tiny attachments on your upper arm, near the shoulder.
You also have a bunch of joints sacs, tendons, bursa (basically fluid-filled cushions) crowded into the tiny space around and between the upper arm, shoulder blade and collar bones. Any irritation or inflammation in that area is bound to pinch things up and hurt. The side to side pain is a clue as to which of those structures may be stressed - but again, if it doesn't go away soon you should probably get it checked out.
We have the sports massage class tomorrow night. I'll ask the instructor if there's anything else he thinks I can tell you!
"If the shoulder is healthy, a marathon shouldn't aggravate it. I would be asking her what injuries have happened to it in the past."
In other words, he thinks it's possible you've woken up an old injury - or since you've mentioned trouble with arthritis it could be related to that. As much as you would prefer to save money, you might not be able to avoid going to get it checked out if you continue to have pain in the joint.