Another propeller shaft out of line on this boat today… judging by the large gap at the bottom, this bearing looks like it is worn. Actually it is quite new but the shaft is badly misaligned with the strut.
The first thing to do is to check the engine mounts. If they are the vertical stud type set in a rubber base, these are the kind that are prone to rocking back and fourth. Check the stud to make sure that its centered in the base with the vessel at rest. If its leaning in any direction, the mount is stressed and the system is out of alignment .
Conduct a back down test. One engine at a time, start from neutral, put the engine in gear and accelerate hard, up to no more than 1/3 throttle. Repeat this process in reverse, all the while watching the mounts for movement. If the engine and mount are moving more than 1/8" in any direction, your mounts are not doing their job of holding the engine in place.
Observe the shafts while running at two speeds, idle and cruise. Observation of shaft runout will only prove the negative; out of line shafts can appear to run true even though out of line. On the other hand, a badly wobbling shaft means something's wrong. Runout up 1/8" is acceptable at idle speeds but not at cruise. If shaft wobble is visible over 1200 RPM, suspect a problem. Again, that's because rotating shafts tend toward self-centering. At high speed even bent shafts can straighten out and show no sign of trouble. If the shaft is observably causing the transmission to move, or you can feel the movement by putting your hand on it, then there's definitely a problem.
Many boat yards think that the way to check shaft alignment is to disconnect the coupling and check the flange clearance with a feeler gauge. That's only part of the story. Before doing this, with the vessel hauled, check the position of the shafts relative to the bearings. Cutless bearings that are worn more on one side than another are a positive indicator that something is out of alignment. Heavy shafts of 1.5" or more will naturally compress the rubber bearing on the bottom side, but not so much that there's an obvious gap at the top.
Next, check the shaft-to-bearing alignment at both the front and back ends of the bearing. If the shaft is off-centered, either to one side, top or bottom at one end, but is off-centered to the opposite side at the other end, then the shaft is not parallel with the bearing bore. It is either up or down, or off to one side. In this case, the whole system should be suspect, at which point the entire system alignment must be redone, including setting up target wire to make sure that the struts themselves are properly aligned.
Now check how the shaft is centered with the opening in the stuffing box flange. If there is little clearance (shaft in the opening), it should be exactly centered; if a lot of clearance, it can be off a little without causing harm.