Thanks for the information Doug. The top holes are close, but the bottom ones moved out from about 7 7/8 to 9 7/8. Yes, the old holes will be epoxyed several times and a hardwood dowel forced in and cut off and capped with epoxy or silicone. Yes, the centering of the motor is important. I plan to make a template or get a Mercury template from a dealer that can hang on the transom. Will do alot of calculations and measuring before drilling the holes. Yes, will evenually raise the motor up from about 1" to 2" knowing that at that height the surface props - Ballistic, PowerTech, and Chopper will work.
Bet you are anxious to find out what you Baja will do. There are always the finetuning, the adjustments, the different feel of a different model of boat.