I have a 2006 GW 222 with a Yamaha 225 four stroke. The bottom of the engine remains in the water when I raise the engine from the water in the marina. Do you know why Yamaha and GW designed the engine in this way?
Depending on how much room you have between the front of the cowling and the motor well, you may be able to adjust the tilt stop so it tilts up a little bit further.
This has been discussed before, bottom line is that boat builders don't really design so that the motor(s) will completely clear the water when tilted up. The bigger concern is that the motor(s) will line up with the hull at the proper angle when running. You can either paint the lower unit cone with regular bottom paint, or buy the spray on stuff specifically designed for motor mounting brackets.
As suggested paint it with anti-fouling paint designed for aluminum outboards - NOT bottom paint that is typically copper based.
My guess is that the raised motor will sit a little differenly when the tanks (fuel and water) are full or empty. If the bot stays in a slip you may want to consider stowing some of your gear forward to raise the transom slightly. This may reduce your concerns.
Mark the water line, then sand, prime and paint the next time out of the water. Petit make an aerosol primer and aluminum paint specifically for that purpose. You still should scrub it regularly as those barnacles are stubborn critters.