Just for future reference, it's "Cutless," a brand name.
The cut in the
fiberglass may need a patch or may be fine with
epoxy as you suggest, depending on
depth and the stresses at that location.
Clean out any gunk, but that's all for the stern tubes. If you have the shaft out, take a look at the surface of the shaft where it contacts the bearings. The goal here is that it be smooth and round, such that you get minimal wear in the soft part of the bearing. Very fine (1000, 2000 or so) sandpaper from an automobile
parts store or Amazon will do that job. If you want to be really Type A about it, make the last
sanding around the shaft rather than parallel to it.
Overall, my impression is that you may be over thinking this. Unless your bearings are being prematurely chewed up by your shaft, inserting new bearings and reassembly will be OK.
Good luck with it.