Typically there are some people answering who do not answer the question but give dumb advice.
The way we did it was to drill the hole in the hull for the propellor shaft first.
The hole should be the same OD as your shaft log.
Next attach the shaft to the engine coupling without the flex coupling after putting the shaft through the hole....you are going to use the shaft as a "pointer"
At this point you have the engine suspended by a come along or chain block and the shaft is attached to the transmission sticking out the hole.
When the shaft is centered in the hole and the engine is at an acceptable angle, take measurements and build your "bearers" or spacers to fit to the existing bearers.
After you have the motor bolted down to your newly built bearers or bed you will insert the cutlass bearing in the stern tube or log and slide it up the end of the shaft (from the outside)
There will probably be an angle mismatch between the flange of the shaft log and the outside of the hull. Mix up some epoxy with an appropriate filler to make the mix stiff enough to hold itself up. Apply this to the area around the hole and slide the shaft log back up to press a "face" into the epoxy mix. Use some plastic on the shaft log flange so the epoxy does not stick to it.
After the epoxy dries you now have a matching face.
Drill your mounting holes for the flange of the log (through the face you just made and through the hull.
Thats essentially it.
Feel free to PM for more details
I'm currently putting an engine in my old Eygthene 24 quarter tonner, i have a Yanmar 1gm10 thats going to go in, as well as an aquadrive flexible coupling that i have come into possesion of, which i will be installing if at all possible to reduce vibration from the engine and stress on the transmission etc.
I have a rough idea formed in my head of how i'm going to do it, but i would like to see other peoples angles on how they would attack the problem, as i don't want to influence anyones answers, i'll state what i was going to do after a few posts have been made. (And any changes i will be making in because of the replies!)
The parts i am looking for advice with are engine positioning, hole location for the stern tube, p bracket location etc, basically the best way to get everything properly lined up or as close to it as possible to minimise wear (obviously the aquadrive will help in this).
As the boat had an engine in the distant past the engine bearers are already in place, and i have measured them as the correct witdth for the engine (pics attached), so really just tips on getting every lined up and in the right place.
Sorry it was so long winded, help greatly appreciated, thanks!