Funny you should mention this - I've been getting shoulder pains after long rides. I've read the same thing too, about shortening the stem, raising the angle, etc. I've also read that putting too much pressure on the arms and hands can transfer road vibration up into the shoulders and neck.
At the moment I'm persevering, and trying to consciously relax my shoulders. There was a good article this month in a British cycle mag which went into great detail about how to set your bike up properly, so I'm intending to check out my riding position with their recommendations.
At the moment, I'm getting a really uncomfortable feeling in my shoulders - a bruised tenderness when I'm riding 50+ miles, which lasts for a few days.
I'm not too outstretched on my bike, as my arms always have a slight bend, even when on the hoods/drops. I've also read that frequently altering your position helps. I'm also hoping, like you, that as I get further into the season my body will adapt.
If you're interested in the article on bike fit, I'd be happy to scan it in and email it to you.