I have run a ton of surface drives over the years. First one was 18 hp, second was a 40 efi, and my current one is a 55efi. The higher the power you go, the more surface the prop runs. With my current set up, my prop likes to be ~ 1/3 out of the water to be running at its fastest and easiest to handle. In turn, when im on plane, my hull runs over shallow sand spots and my prop doesnt even touch. I can feel the hull go over these spots and my prop never even touches or catches, and I feel it a lot in one of the spots I hunt. Its the only reason I have a surface drive, otherwise every other hole I hunt, I can get to with an outboard. That one hole has just been so good to me over the years, so I cant give it up and go to an outboard. Careful with this, not sure I would want to hit a rock at speed and my hull being the one that takes the impact. I hit all kinds of stuff with my prop though when idling around or half throttle. I usually have to get a new prop every year, but more from the sand I run and it just eats away the blade. I have no experience with long tails, but I dont think I would ever consider one anymore with how good the surface drives handle, and the maneuverability of getting turned around on a dime.
I too would look into a jet drive if rocks were you're primary issue and concern. You would also get that outboard torque and likely better performance. If you decide on the surface drive route, I would go as big as you can afford and have a spare prop on hand at all times. I think I have 2 extra in my boat. One from previous season, and one for big heavy loads, but in a pinch, both would get me home if I had a failure of any kind. Never had that happen, but would rather be prepared than not.