OW stroke question

I was an age group swimmer through high school, and then I dabbled in water polo in college. Playing a lot of water polo, I started to have impingement problems in my right shoulder. I laid off swimming for 8 years until I was 30 and really overweight. Got back in the pool for a couple of years and quit again. No problems with shoulder. When I started swimming again about four years ago, I started to have the impingement pain again. I decided that at 35, perhaps I needed to stretch. I looked up specific stretches for rotator cuff and began doing them. No problems, other than a slight ache after really long non-stop free style swims (3K-5K). But these aches cleared up after a day of rest. Thus far, all open water swims I've completed have been in relatively calm lakes. It's easy to maintain a streamline, use a decent body roll that eases stress on the shoulder and get the most out of a 2 beat kick (mine's a bit funky; almost a four-beater). Last week, I swam a 2-mile non-stop (my weekly schedule alwyas includes one long swim) at the Y pool (25Y) in which I train. I started off in the pool alone, but when I reached 1000 yards to go, I was splitting a lane with one of the one stroke followed by controlled drowning and repeat wave machines, and outside of my lane was a large water aerobics class. What was calm water became really choppy and wavy as it was crowded with new years resolutioners and not subdued by slack lane lines. My streamline broke. My stroke shortened as tried to get my fish-tailing legs back in line. I fought the pool for the last 1000 yards. And both shoulders hurt for three days in that area of impingement pain. I'm cool with the pool getting full and wavy, but this spring I am hoping to do the Pensacola Bay Swim (3.1 miles) which can be choppy (hope to repeat the Big Shoulders which I guess could be much choppier than the glass like conditions we had this go round). I have concerns about my shoulders safely making it 5K in choppy water with a broken stroke. What do you OW swimmers who routinely swim in such chop (as opposed to big swells which I can handle) do to alter stroke? What's different about your stroke as opposed to swimming in perfectly calm water?