Thanks for the help so far. It seems that I am not the only one with this generator issue. I talked to the generator company and they acted as if they had heard about this problem many times before. They recommended a power conditioner ($200) from another company. As to how I hooked up my furnace, their are several ways. But my power was out and the quickest at that time was to open the switch on the furnace and wire directly into the furnace, bypassing the home electrical input but leaving the ground attached.