Seems like a lot of 'what-if's' out there. I had issues with my inboard Atomic 4 on a 1970 Cal 28. Decided to go the outboard route instead of hassle with another rebuild. I use a Yamaha 9.9 High-thrust model with a 25" shaft. I've used two mounting options- both the inboard well and a sailboat outboard bracket.
For the outboard bracket:
Pros: Easy to get the motor on/off, tilt-up available, easy to flush after sailing (lean over the side and attach the flushing rig)
Con: Hunk of metal hanging over te side.... It looks like all auxilliary outboards, not quite as pretty. Maintenance was sometimes an issue, especially with small parts. I rigged a catch bag around the motor to prevent losing stuff to Neptune
Pros: Looks sharper, less chance of losing tools (although they fall through the hole just as easy) and the fuel/control lines were shorter
Cons: Difficult to pull out/ put in, since it required a lot of wiggling to fit into the factory cut out.
All told, I got 6-7 kts in the harbor, 5-6 kts open water with the 9.9, vice 4-5 kts with my Atomic. I reinforced the transom with 1"x6" oak planks where the bolts for the outboard bracket went in. I saw a little flex at full throttle. Using yamaha cables, I used my existing engine controls, then rigged a new fuel tank. The old one leaked and the boat smells better inside now.
I noticed little change in pitch with the extra weight on the stern. With the Atomic out, I've got extra storage for stuff and noticed better sailing characteristics with less weight. This boat has 2200 lbs of encapsulated lead for ballast.
Good luck with the decisions, it's tough. I did all the work myself and it definitely wasn't all clock work. Then again, anytime I had questions I just asked the local outboard shop and they had great answers. Total cost was around $2500 for everything.