Yeah do it that way it will transform the boat and because there will be no strakes (I hope) on the the pod it will not force too much stern lift, make the trailing edge as sharp as possible, none of this rounding crap for aesthetic purposes.
Good luck big job ahead if you decide to get at it.
Just one thing consider leaving the back off the centre portion if possible (long shaft?), with a full width and length pod you may? find the boat a little buoyant at rest depending on what it's like now but could also depend on the weight ofengine fitted also.
cheers fnq