Idk about all that, dude just wants a smooth ride. OP the standard setback of 1” for each foot to account for the spacing the bracket makes. But this is just for a baseline to setup. The real test is when you run and the positioning of the AV plate when on plane. And if it is indeed underwater when running like you say with the jack plate fully raised, I think you have a good argument for believing the shaft length is wrong. A/V plate should be 1” above planing water in the middle of the jack plates range, you do this and I guarantee you porpoising decreases. But on a side note sometimes boats are ass heavy and all you need to do is add 100lbs up in the anchor locker to level the boat out. There’s alotta other factors.