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Listen to mb466. Too much weight in the stern can ruin a great boat. The Yamaha F90 is a very heavy 90. I would not put it on a jackplate at all; it will only upset the weight distribution even more.

I would bolt the motor to the transom as high as it can go, use a good prop (like the Stiletto Advantage) and avoid having a kicker motor at all.

Moving the battery(s) to the console will help.