I think I'd just remove about half the fuel and fill it back up with straight fuel so you'd have a mixture that would only be about 100:1 and I don't think it would hurt your new 4 stroke a bit, but ask your Yamaha dealer if you want to be sure. Then, as your tank gets empty, gradually burn the mixed fuel you removed. As for protecting your engine, if you haven't been having fuel trouble with your old 2 stroke, you don't need to worry about your new motor either. I'd add an inline, water separating, fuel filter before you run your new engine, but other than that, I don't think you need to worry at all.
If you don't have an easy way to remove the old fuel, just take the mercury fitting off the end of the fuel hose to your old engine, set a 5 gallon tank on the ground behind your boat, and squeeze the bulb as if you were priming your engine. With the end of the hose as low as possible below your fuel tank, as the fuel starts to flow, it'll keep flowing until you raise it higher than the boats fuel tank.