The engine, the gearbox coupling, the shaft, the shaft seal and the cutless bearing in the strut all have to line up. When they don't, the shaft bends a little on every turn. The cutless bearing wears fast, the shaft seal leaks, the boat vibrates, and in the end the gearbox or the shaft fails.
How a surveyor spots it
A surveyor doesn't usually measure alignment. The signs show up on the sea trial and the haul-out.
Under way. Vibration through the sole that rises with rpm. Watch the shaft between the seal and the strut at idle and cruise: a visible whip means something is out. The late surveyor David Pascoe accepted up to 1/8 inch of runout at idle on shafts of 1-1/2 inch and under.
Engine mounts. Pascoe's back-down test: a short, hard burst ahead and astern while someone watches the engine. If the engine or a mount moves more than 1/8 inch in any direction, the mounts have failed. See failed engine mounts.
Out of the water. A worn cutless bearing, especially worn on one side; a strut that moves when struck with a block; a galled shaft. See worn cutless bearing.
Records. A new engine, new mounts, a grounding or a refit without a record of realignment.
How alignment is checked
At the coupling, with the boat afloat. Steve D'Antonio describes the method: separate the coupling faces, check the gap with a feeler gauge, rotate the shaft half a turn and check again. His limit is about 0.001 inch for every inch of coupling face diameter, so no more than 0.005 inch on a 5 inch coupling. The engine is moved on its mounts to close the gap.
Both D'Antonio and Pascoe say final alignment is done afloat, because the hull changes shape when hauled. D'Antonio estimates that well over half the boats he sees have some misalignment. Pascoe warned that a coupling check alone can give a false sense that all is well, so the strut, shaft and mounts get checked too.
What decides the grade
A whipping shaft or a loose strut is an A, and so are mounts that let the engine jump: the shaft or gearbox can fail under way. Vibration, a fast-wearing cutless bearing and a seal that won't stop leaking point to a B. A missing record after an engine change is a C.