Mayber it's just me but I'd far rather have the O/b in a well. I have a Cal 21' and the O/b is mounted on the transom where it can easily come into contact with the Cal's rather long rudder. You're also likely to have as much fun beefing up the transom as you would reconfiguring the well.
Don't miss this thread and Jim H's link within it for an amazing well displayed and well done restoration of a mighty Cal 20. Cal 20-- Excellent Starter Boat
Try a bit of bleach in your cleasning solution for the black spots. It shouldn't be a real strong solution to do the job and probably will not do much to harm what is no doubt already pretty faded gel-coat. (g) If the deck is painted it probably will do little if anything to hurt it. Once the mold and mildew are killed they clean up a bit easier. Clean it up well and then get some non-skid wax on it soonest for future protection. "Woody" wax seems to work well as a non-skid wax.