It is a PIA and somewhat costly job but it will work and as far as performance goes..it should increase. Generally, outboard propeller efficiency increases a little bit to a sweet spot a couple feet aft of the transom. I don't know the exact sweet spot (a bracket manufacturer might though) but you're headed in the right direction.
Instead of doing all that...just buy a boat made to take the kind seas you plan to fish. If your feet are getting wet..that is a hint.
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