I'm not sure where to start here, but you don't want to be guessing how much your shoulder can handle on meet day. Opener should be something you know you can nail (even on a kind of crappy day), second attempt what you need to get your goal total, and third attempt go for broke if it's a good day.
Option A: You wouldn't need to worry about your shoulder as much in a high-bar position as you would in a low bar position. You sacrifice some leverage and therefore weight with this position (because of a tendency to fall forward), but if your shoulder can't handle the low position anyway, I guess you're not really sacrificing weight.
Option B: If bar position isn't what is affecting your shoulder, you've still got to establish your weight/shoulder injury tipping point. The only way I can think of to do this is to use the barbell for your 5/3/1 sets at the low training max. Then, do jokers to find out what you can handle. Extra reps the final 5/3/1 sets probably isn't the best idea because you wouldn't want to fatigue the shoulder joint before attempting the heavier singles, but that's your call. Any extra volume could/should be Zerchers for similar reasons.
Option C: Do your working sets with Zerchers (still without the extra reps), then ramp up to a few single's with the back squat.
Best of luck at your meet,