All shafts will have some deflection due to the shaft weight--this can be calculated. However, if the engine has been in alignment in the past, all you have to do is to bring the two coupling halfs together--often there is an indent on one coupling and protrusion on the other to allow mating. You then start with the feeler guage on all quadrants of the coupling. Then adjust the engine side to side, up and down, fore and aft mounts. If the shaft has not been aligned, then in today's world a lasser can be used to find the center of the transmission coupling sighted up from the cutlass bearing and thru any intermediate bearings. One other comment on alignment--yes the Drive saver does help with minor misalighment--but not for gross alignment. Engine mounts are not forever--they need to be replaced peroidically--and many used boats I have looked at had old worn engine mounts--just another part of maintance. I prefer that the engine beds have steel bearers running the entire length of the stringers, so you are not dependant of "soft" stringers. Some high speed hulls may flex, but most trawlers should be built so that in normal use there is little motion of the hull itself. Regards, Bob Austin