It's never a simple answer Ryan. There are many scenario's to the problem, some are possibles, some a probables and some are a mixture of inevitables.
First of all, even a .005" difference can be translated as a greater error at the opposite end. If the opposite end is tightly held, then that error has to be corrected somewhere along the shaft. It can be seen as a bending of the shaft and a thus a incorrect stress/wear load on the bearing. It can also be seen as a vibration. This part gets complicated. But it is to do with the load being transfered to the shaft via the prop blade. The less No. of blades, the more the problem. It works like this. The driving force is seen on a blade, as it is basically a rotating padel. On a two bladed prop, the blade opposing is also creating a driving force. This "push" is seen out on the face of each blade and is transfered to the shaft at opposing sides. But the two area's that have no blade, has no pushing force. Following so far? OK, so if there is inbalance along the shaft, the Pushing force can help to counteract that balance for two opposing 90 degree area's of rotation and can cuase the vibration to increase at the other two opposing area's of rotation. This force will change at differeing RPMs, thus differing rates of force. Max bend in the shaft could be seen at max RPM. You could try one method, of turning one half of the coupling 90 degrees. Thats just one set of bolt holes around. This places that vibrational stress on a different area of the shaft. But remember, that may or may not be the problem.
The flexible coupling does many jobs. Firstly, it helps to take the stress off the components from that alignment error. Secondly, helps to take the stress off components from any error arising from the prop itself (maybe cavitation, hitting a piece of debris, blades being slightly uneven in producing equall force etc) Thirdly, it reduces vibrational noise
from two directions. One, the engine. The engine is a source of two distinct vibrations. One is just plain torsional movement as load variations cause the motor
to flex in its bed
. The second one, and one that is not commonly realised, is a phenomenen called "injector shock". This is a shock wave sent down the crank shaft and onto/into anything connected to it.
The other direction is from the propellor, back towards the engine. Remember that in most set ups, the driving force of the propellor is coupled to the hull at were the engine meets it's bed
. So any vibrations produced out at the prop, which can be caused by many many things to do with the propellor and the hull, is transmitted to the engine. The flexy coupling helps reduce this noise
being transmitted to the engine, thus to the mounts, thus to the hull. Oh and the mounts are another area. The wrong mount for the engine or a mounts that have lost
there strength or been damaged by oil
etc, will not isolate transmitted noise either.
IMO, no engine should be connected to a shaft without a flexy coupling. No matter how exacting, there are too many other influences that just can not be compensated for without a flexy. Andy yes Flexies are expensive, but once again IMO, the expensive wear created in other area's with out one, far outways the intitail cost of getting one.