How to Measure Outboard Shaft Length

An outboard's shaft length has to match the height of your transom, or the propeller runs too shallow or too deep. Measure the boat and the motor the same way, then compare.

Measure the transom and the motor the same way, top of bracket to plate.
Transom: top to hull bottom. Motor: clamp bracket to anti-ventilation plate.

Measure the boat's transom

Measure straight down from the top of the transom, where the clamp bracket will sit, to the bottom of the boat. Do it at the center of the transom, since that is where the motor mounts.

Measure the motor

Measure from the top of the clamp bracket, where it rests on the transom, down to the anti-ventilation plate. On a Yamaha, the identification label on the port-side mounting bracket also gives the drive shaft length.

Compare the two

The motor's figure should be a little longer than the boat's, so the plate sits slightly below the bottom of the hull. Honda wants the plate 0 to 2 inches below the bottom of the boat.

Check it on the boat

With the motor clamped on and straight up and down, Yamaha says to lay a straightedge along the keel to the outboard to see where the plate sits. Raise or lower the motor if needed, then tighten the clamp screws again.

Measure from the top of the clamp bracket, where it sits on the transom, down to the anti-ventilation plate just above the propeller. On a Yamaha, the label on the port-side mounting bracket also lists the drive shaft length.
Measure straight down from the top of the transom, at the center where the motor mounts, to the bottom of the boat.
It is the shaft class. Mercury's FourStroke 9.9 comes with a 15-inch short or 20-inch long shaft, and Honda's BF200D to BF250D come in 20, 25 and 30-inch versions. The exact figure differs by model, so check your owner's manual.
Slightly below the bottom of the boat. Honda says 0 to 2 inches below, Mercury's small portables 1 to 2 inches, and Yamaha even with the bottom or about an inch below.
Yamaha says the motor has to sit deep enough for cooling water and for the propeller to work well, but too low adds drag. It warns that the wrong height can throw spray that starves the engine of cooling water.
It depends on the motor. Mercury's 150 FourStroke manual caps the mounting height at 25 inches for L models and 30 inches for XL models, and wants the exhaust relief hole at least an inch above the water at idle.