I ran mine for 2.5 hours at 35 to 50 mph in 2-3 waives from St. Pete to Captiva Island over the holiday and the generator ran perfect. I don't think moving the water pickup will be that big of a deal. Teague Custom Marine even has a transom pick up that is adjustable to get the right amount of water to the intended target. Good luck.

Instead of moving the pickup try a larger sea strainer first. Maybe it will hold enough volume to compensate.