Been there. If there are no exhaust leaks or fuel leaks there should be very little odor. We had that problem and tracked it down to a small fuel leak. A little diesel fuel on a hot motor vaporizes and stinks up the boat. So I would look for leaks and fix them. Another strategy that we used was to run the bilge air blower while running the motor and for a little while after shutting if off to move a lot of fresh air through the engine compartment.
Those things either worked, or we got so used to it we couldn't smell it anymore.