+1 for the tunnel hull recommendations. Certainly great for shallow water running but most importantly great to get that foot up as high as possible. Everywhere I go, the motor is way up and sounding like a Harley.
Something you might have to comes to terms with in fishing the aforementioned areas (some more than others) is the inevitability of hitting a rock. If you fish enough, its going to happen. Hopefully you are idling slowly when it does..
I also recommend getting a nice/wide GPS with FMT. Not all the FMT tracks can be trusted so find safe passage, save the path and do not deviate from it. Just like any other area, most learning is accomplished when the motor is off anyways!