3" slugs give you either a heavier slug, more velocity, or both. And always substantially more recoil.
Unless you are hunting bear, 12-gauge slugs are already overkill for deer and there is no rational reason to use 3" slugs unless you are trying to squeeze an extra 30-40 yds of useful range at long distances.
I have never hunted with a 3" shell.
Fire 2 shots at 50 yds. If they are close to each other, and assuming your scope is 1/4" at 100yd clicks, measure the distance you are low from your aiming point in inches (to the center of the group). Multiply the number of inches by 8, then add 16. Go up this number of clicks. This should put you 2 inches high at 50 yds. You should be able to now fire your 3rd shell at 100 yds. Measure inches from desired POI, multiple by 4, and move that many clicks in the desired direction. Fire your last 2 shells and they should be about where you want them.
You have now roughly sighted in with a single box.