All of my mudmotor experience is with GD longtails and SD's on the interior rivers of Alaska since 1988. A lot of my running is in shallow, gravel bottom with the largest rocks about the size of softballs. The basic rule is "if the boat will float, the motor will push it". I like a boat size of at least 18 X 48 because it will carry a large load and still go shallow. The boat I use for long trips is 24 X 48 with a cabin on it and a 35 GDSD. I have run jets and the only advantage, I have seen, is if you have enough power they are faster, but they burn 2 to 3 times the fuel per mile and they are very difficult to get on step from a stop if there is only an inch or two of water under the boat. Obviously, if you get in mud, weeds and brush the mudmotor has the edge.
The answer to your question is yes, a mudmotor will work in your shallow rocky streams. If you are going slow they will go shallower than a jet and get better fuel economy. When you do smack the bottom a mudmotor with a steel lower unit is more forgiving than an aluminum jet foot. If speed is important, a big jet will be faster. Even on the big rivers like the Yukon I prefer the mudmotor because of its reliability and fuel economy, but I'm old and don't need to go fast any more.
