There is evidence that the particulates in diesel exhaust can trigger sinus problems. This Google search lists some scientific studies. Possible solutions include:
Try a respirator mask. This Honeycomb Carbon Mask claims to be effective against diesel.
Extend the exhaust pipe so the fumes are blown above head height. Fix a vertical pipe to the side of the tractor and connect it with a flexible pipe to the exhaust. As the fumes are ejected a few feet above the pipe, the top of the pipe does not itself need to be at head height.