You can do this out of the water, you just have to take into consideration that the rpm are going to drop with the added back pressure so you will have to set it higher out of the water than when it's in. I don't remember if those have an idle set screw like the carbureted motors do. If it does it'll be pretty evident as it's a screw that adjusts how far the throttle can go back on the side of the engine. Engine RPM should be close to 1000 in neutral. The clunk you here is normal though, although in your case probably a little more severe. If you can't figure it out yourself, or you doubt your knowledge be safe and take it to a dealer.