I read on misc.fitness.weights that somebody's shoulder problems were partially caused by inadvertently slouching while sitting in front of a computer for hours each day at work. When they made a conscious effort to hold a properly upright posture, it helped. I'm probably doing the same thing, so that's something else I can work on. I've also started working on not leaning to one side or another when I'm standing, as I've heard that that can lead to trouble. I have some weird ways of standing, so perhaps that was contributing to my lower body owies. As dymphana mentioned in a comment elsewhere, if you have a strength imbalance, other muscles will try to compensate for it, leading to more imbalances and other nonfun shit. You'd be surprised at the effects of seemingly trivial quirks of posture or biomechanics. One of Rando's dad's legs is a few millimeters longer than the other, and that was enough to give him back problems.
w00t. Earlier, I had located this helpful page of exercises for hip muscle imbalances (which I thought would be useful because I failed the prone leg lift test on that page). I poked around the site some more and found a page on preventing shoulder injuries, which suggested looking for trigger points where the pec meets the shoulder - a spot I hadn't even considered. I started dutifully prodding my right shoulder in that area, and lo and behold, I found an owie. A few seconds of pressing said owie temporarily released the tightness in my shoulder. Yaaaaaaaay! I'm going to sit my arse in front of the tube and work on prodding myself for a while. I should at least start the middle arm guard piece pattern, too.