1999 BayLiner 235 Overhaul

Recently I bought a 1999 235 Bayliner Bow rider. I will be Overhauling the Entire boat including Buying a new Motor and Stern drive. The 235 comes with a Mercrusier / Gm 350 / Carbureted and an Alpha One Stern drive. My question is should I replace the Sterndrive with a Bravo or go back with an Alpha One? Will the hole in the transom be the same for other Stern drives? I plan on keeping the Engine the Same size but that can change to. I guess what I'm Getting at is I would like some suggestions on what Configuration I should go with and why? I am very new to Boating and Boats in general so any information would be greatly appreciated. I also would like to know some thoughts on Fuel injected or Carbureted.
Thank You
Duane Perry