Had the same problem with a flexable coupling on a 1" dia shaft and getting the coupling off the shaft, tried hitting it, pullers, heating it, no chance.
Then told an old trick, undo all the coupling bolts enough to put a 'large socket' (bigger i/d than the shaft) between the two coupling flange faces, re tighten all the coupling bolts, you then push the couplings apart no problem !
The flange on the end of the shaft usuallly has a key to locate it, so don't lose it in the bilge!
Also check most flanges have a grub screw, pin or bolt locking it, so make sure you have undone them before starting.
As Tim said the stern tube rubber seal is not ordinary rubber piping, it is special thicker walled especially for the job.
Good luck it's fun!!!
Archivist for the Colvic Watson Owners Group