[GeeWhiz]

My Comfortmaker furnace is a model GNJ075N12A1. It is about 8 years old. It is not a "high efficiency" model, but it has a combustion blower motor/fan or sometimes called "inducer fan" that assists the exhaust out the flue pipe.
Recently it does this same exact thing, especially after a lengthy cycle of heating up. At first I thought it was a particle or fragment that was caught in the fan wheel, but now I'm not sure. It is a fairly rapid, uneven clicking noise--like you described.
I described the sound to a furnace repairman, and he thought that maybe the "high limit cutout" switch was activating and shutting the furnace down.
Macman4, did you ever find out what caused this problem in your furnace?
Thanks,
Quent