did you have to undo your prop shaft coupling to do the job on your transmission? if so , check that you followed the install directions on torquing down your coupling bolts. most manufacturers such as centa tell you to reinstall the coupling using a torquing pattern of #1-#4 to half the final torque then # 2- #5 then #3-#6 to half, not 1,2,3 then 456 cranked all the way down. Then do #1-4 , #2-5 etc. to final torque. this #1-4 pattern with 2 steps to the torquing keeps the coupling halves evenly bearing down and equally torqued around its circumference . that pattern will avoid the misalignment of the coupling which could be caused by cranking the bolts 123 totally tight to final torque then moving to 456. torquing the coupling down that way 123 could possibly be causing your .003 faceout.
if the old motor mounts gave you an aligned shaft before the transmission repair, i'd be surprised that you now need to adjust them to cure the faceout. have you measured face out at 12 oclock, 3 oclock, 6 oclock 9 oclock on your coupling ? am i understanding that only one of those measurements is 'out' .003? what are the other faceout measurements?
before you mess with the mounts: can you figure out how many threads are engaged on your existing motor mounts both left-right and fore- aft ? look at the nice picture posted by capejt. I'd mark the existing positions with tape before you start adjusting threads .
without access to a mechanic for a couple weeks i'd start at the coupling and redo that joint, use a torque wrench to make sure you have the right torque. see if you can closer to the desirable . 001 each of the 4 positions.. after that exercise if you have threads left to adjust, it should be a simple matter .
how old is the engine install on your boat, both in years and hours of operation? yanmar used to r ecommend installing new motor mounts after only 5 years chronological age as their soft rubber mounts would bottom out and the proshaft could go out of alignment. I didn't find it necessary to redo the mounts every 5 years but by 20 years, the mounts could not be adjusted any further and the mounts needed to be replaced.
MitchM
Nauticat 321 Eagleswing, port of Erie PA