We had the same problem. After a 2 hr leg I always used to get a bit of a rough throat and headache. I mentioned this to one of the other owners and he said he had the same. There was a bit if a smell in the cockpit too, so one day we did a test flight with a CO detector. Lo and behold, 30 minutes into the flight the thing went off....I was going to borrow my plumber friends gas analyser to get a reading but then after some investigation we figured it out.
On our aircraft there is a belly panel which is removed for the annual. It should slot in above the engine cowling but when they had put it back it was not....so there was a small gap. The result was that the exhaust was seeping in between this panel and into the floor space and eventually filling the cockpit with exhaust fumes. Once this was rectified the problem stopped.