Might cross post on the Capri 16.5 Yahoo Group (groups.yahoo.com). I think I saw a similar post back when we had our Capri 16.5.
I agree with FastOlson - the Capri 16.5 has quite a bit of windage in the bow and putting that motor on the port quarter will only make it worse. I used a Group 27 battery & Minnkota trolling motor and the stern squatted pretty badly. It was in the center though, between the scuppers. If we'd kept the boat I was going to move the battery up into the cuddy to help balance things.
If you use the bow eye I'd double check to make sure the backing is plenty beefy (can't remember what they use) and probably rig it with some kind of rubber snubber so it reduces the shock loading. If you don't want to tie the motor in the middle of the cockpit (not sure I would) maybe think about putting it up in the cuddy. There's plenty of room and it might just be low enough to help keep the boat from flipping over.
You might try mooring with the centerboard up. I bet the boat is sailing on the mooring and getting tripped over the centerboard. Without the CB it should skip across the surface better. IIRC we always put ours up at the dock.
There's no backstay but I bet you could rig an anchor riding sail. I made one for Verboten that ties to the boom, a cleat near the base of the mast, and uses the main halyard for the top.
Another thought, if you're actually going completely over, would be to get a Hobie float or hoist a gallon bleach jug up the mast to keep it from going turtle.
Hope you get this figured out; the Capri 16.5 is a fun boat. I'd have kept ours if I could afford 2 boats.