Dave, how old and what kind of furnace do you have? A rather continual headache (you and your wife) + sore thoat could be form of carbon monoxide, fuel not being burnt cleanly. Do you have co detectors? Man it ain't nothing to mess with as I'm sure you realize. It wasn't an issue while you were away, but when you returned?............. Call your local fire department, they'll gladly come and do a complete test and It won't cost you a dime. Just call them, explain and they will tell you exactly what to do/not do until they arrive, and this is very important for an accurate test. Make the call !