I actually understand your difficulty, on our boat the settlement over time of the mounts was such that the shaft was rubbing on the shaft tube. And you can't tell that with the packing gland in place. So, how do you verify that the shaft remains in the center of the tube? Since the packing gland and the engine
mounts are all flexible. Short of a bearing to hold the shaft in place you have to guess.
On our boat we aligned (out of the water) with the gland open so we could see that the shaft was in the center of the tube. Then we put a mark on the shaft and took some caliper measurements from the shaft to the hull/keel. Wrote those measurements in indelible ink right on the hull
. For port/starboard we just eyeball as we can see down on the shaft/tube, but for up/down we use the measurement. Can detect a change of about 2mm (I'm not a perfect machinist) which still keeps the shaft pretty much in the center (we have 6-8mm annulus). Then align coupling as per normal. We now check once/year against the measurement to see if the engine
is settling on the mounts.
[Edit] another technique I've seen, but doesn't work
in our space, is to put a laser pointer on the shaft and then mark a target somewhere. In the water you can then check to see if the same pointer has shifted up/down compared with the target. Usually takes a bit of shaft run to make that work
, we don't really have the space.[/edit]