I would think there would be options that would work without going from cable to throttle by wire.
You say you want to repower your boat. What do you have and what do you want to go with?
Re-powering doesn't have to be some crazy over the top rework but you'll have to stay within the limits of your current ECM. That said, you're going to need to change the CAL file but with out a dyno or some sort of data logging you have no chance at getting it right.
You may want to contact Arizona Speed and Marine. They do custom tuning for boats.
What are your reasons for wanting to change the motor?