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.



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All in all, the pain in my upper body (neck, shoulders, upper back) is minimal, only what was already there from life in general, so that is a huge improvement. I used the advice I found...somewhere on line...anyway it said, measure your shoulders bone to bone in centimeters and buy a bar exactly that width. Mine were 36 cm, but I know I like a wide stance with my arms, and my previous bar was a 44 cm so I thought it would be too huge a jump and opted for the 38 cm. so far so good!
Yup, the mountain bike gets me moving around almost all the time. I think like a border collie on it - ever watched a border collie run through anything bumpy? when you watch them, you can't tell they're going over high and low things, they just move their legs up and down to adjust, and the top of their back pretty much stays at the same position all the time....like the cosmic crunch up a bumpy climb... very cool...