What you have to consider is that a 25hp outboard weighs about 120 pounds. A boat of this size typically has a 15 hp limit on it. Sam designed the boat to work with a larger motor, which it does well.
The newer hyper lite motors in the 14hp model will max the boat out by weight and not power. You can modify the build a little to make the stern wider to float a little more engine. You will have to not build in the motor well in order to use any of the mud motors. The one issue that I can think of is that even though the BB3 is a "planing" hull, it still has some rocker to give it stablity in rough water. This rocker will work against you using a mud motor since they are weak when it comes to pushing water. They work great pushing mud, but I have been "stuck" in a sled with a 32hp prodrive when the boat at low speed had its bow up on a stump. We tossed up a wall of water behind us but that 4 inch stump stopped us cold. I had to get out and lift us off the stump. Once up on step the mud motors do well, but getting the bow up with a mud motor on a BB3 in water may be a chore once the boat is full of gear.
You can call Sam or Joe and they will talk you through the changes that you are considering.
For my BB3 I am using a large jack lift to keep the motor up and run it shallow using the motor well as sort of a tunnel to feed the prop. It is a slow messy shallow water solution, but I don't have any mud to run a mud motor in, just weeds, which I can handle cleaning off once in a while if I have to.
