How to deal with paint fumes from 2-pack paint?
The fumes are not isocyanates.  Once the paint cures fully, there will be no isocyanates in the paint.  Let me explain where the isocyanates are (or were) and how the paint is toxic. 

To oversimplify, paint contains three parts: 


Pigment - the stable material that gives paint its color. 
Resin - the glue-like binder that sticks the paint to the surface and holds the pigments together.  This stuff cures like epoxy. 
Thinner aka reducer - which makes it thin enough to paint, then evaporates fully (dries), and is gone. This is the "paint stink". 


Pigments used to be hazardous. But since they are part of the paint forever, and they become microscopic dust when you sand paint, the government made toxic pigments illegal long ago. 

Thinner/reducer has toxicity like similar chemicals like gasoline, toluene, etc.  That's why you should not paint in a confined area. The stuff used in 2-pack paints tends to be nastier and more stinky.  And yes, it will give you a headache.  When it evaporates, it will be gone. 

If you want to know exactly what it is, look up the brand of paint (likely Interlux or Awlgrip), figure out the reducer recommended for that paint, and check the MSDS (material safety data sheets) for that reducer.

Resin is designed to "polymerize" as it cures: join with nearby molecules to become a much longer molecule.  With 2-pack resin, they simply contain an A and B part which connects sequentially: ABABABABA. The B-part contains BPAs or isocyanates which have receptors on each end of the molecule, which will aggressively "grab" the A-part.  This makes it polymerize fast, in mere days.  At that point it is no longer isocyanate, and its atoms have become part of a much longer molecule that is too large to be liquid or vapor.  You're not smelling that, obviously.

Isocyanate is a cumulative toxin which can inflame or damage the immune system.  Painters get exposed to it thusly: 


Spray guns atomize the paint resin into a fine mist.  If they don't use proper protective gear, they can breathe it into their lungs, which are very vulnerable. 
Sanding dried paint which hasn't fully cured, and getting the dust in their lungs.
Brush/roller application is pretty safe since the resin is not airborne.  


So how does that impact you as a boat owner?  The isocyanates aren't much of a threat to you.  It will be almost entirely cured after 3 weeks, which means the isocyanates are gone.  Like epoxy, it doesn't need fresh air to cure.

The fumes will ultimately dry and go away.  It helps to air out the boat; and/or it helps for the boat to get hot.  The fumes are heavier-than-air, and will want to go to lower parts of the boat.