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Drag and lots of it. Even boats with properly matched motors can pick up a few miles an hour but raising the motor an inch. I can't imagine how detrimental sticking extra 4-6" in the water would be. I'd add a jackplate if you really wanted to use your long shaft on a short transom.
One other thing to consider; some long shafts can be converted to short shafts. The cost is usually prohibitive, but just wanted to throw that out there.
I thought about converting to a short shaft but, the short drive shaft was 200 bucks, and then I need a short shift rod connection. It's a 1976 25 hp Johnson, a good motor, but not really worth the extra money it would take.
just a rough guess, it depends A LOT on the boat, but having 4-6 extra inches of metal in the water is going to cost you at least 20% of your horsepower, with INCREASED fuel consumption. The smaller the boat the more pronounced your loss will be.