Hi Curt 233,
I am sorry to hear about the the State of your ship, if you can't get the owner to maintain the ship in a safe condition to work on board, I would find another job and then tell Transport Canada etc about the problems.
You could be seriously damaging your long term health. "Vote with your feet" as we say over here.
I am surprised that there isn't some sort of flexible expansion piece in the exhaust line after the Turbo, the expansion in the exhaust line from cold to full power is considerable, I don't think that I have ever seen a Marine Engine of any size or type without one. Sometimes the bellows pieces are enclosed in a sleeve that is welded to the flange at one end and free to expand at the other. You can usually find the expansion piece easily because the bore is the same but the outside diameter is larger. If there isn't an expansion joint I should imagine that the repeated stress would cause cracking in the exhaust pipe due to metal fatigue.
Good Luck, and if you can't fix it, get the Hell out, and if you don't tell Transport Canada about the problem, you will be putting your replacements health at risk because so long as he is working there he won't be able to "Shop" the owner either.
It is always better to ask a stupid question than to do a stupid thing.