I'm no expert but from what I've read, I don't think the small stride is a problem - it keeps your body centred over your feet and gives you a faster cadence, which is supposed to be a good thing, I think.
I know what you mean about the upper body stuff though. I think my arms are ok but I have been making an effort lately to have shoulders back, chest out and, most of all, head upright. I had a tendency to have my head forward/down too much. Which, if you think how heavy your head is, must be bad for your centre of gravity and put pressure on your neck / back. I find I tire less easily now too - carrying your head in that position instead of it sitting on top must add to your overall effort.
This probably sounds really daft 
but when I first started trying to change my stride and posture, I always had in the back of my mind (on longer runs) the bit in Born to Run where he talks about tribesmen being able to hunt down, and ultimately catch, a deer/gazelle type thing. I sort of pretended to myself that I was doing it . So... light on the balls of your feet, slow steady pace, head up as if to scan the horizon, running at a speed where you feel you could keep going for a looong time, just keeping the deer in sight until it tires, not actively trying to catch it, shoulders relaxed, arms bent at a loose angle. That kinda thing. But the head position is the thing that seems to make the difference for me. and 
at the idea of me being able to catch a deer.
Sorry for the epic post when I should be making the dc's packed lunches. I guess it's nice to chunter on about running in the absence of feeling well enough to actually do it!