Stephen,
My housing is the original that came with the boat (2005) and
our drive trains probably are different. My stern tube is
about 5 feet long since the engine is mounted under
the galley sink which is a few feet forward of the companionway.
The first time I replaced my cutlass bearing I was going to
remove the housing (totally unnecessary). My fear was
spinning the housing mounting bolts that were bedded into
the hull. The other one was creating a problem similar to what
you're experiencing.
It sounds like your options are limited if you can't satisfactorily
re-mount the tube to the housing.
Other then the stern tube length and the the type of shaft seal,
traditional stuffing box or dripless etc., the way our
tubes are mounted can't be that different. I don't know
what difference internal or external threads would have at this point.
If you end up having to remove and replace everything let us
know what you come up with. I'm sure some of us will go
down the same path eventually.
Good Luck,
Nick