Clunk noise Ruud Furnace

I had the same problem, the motor shaft and bearings were going bad. There was about 3/16" travel on the shaft that the blower attaches to. I replaced the motor myself and it runs nice and quiet. I have had that noise that you describe for over 8 years, but it got real noisy about a week ago. I talked to the maintance department about it where I work and they said the motor bearings were probably going bad. They were right, I took the motor out of the furnace and they took it to a parts store and got me a new one $270.00 for it. It is a special motor due to the fact that the frame mounts bolt directly onto the motor housing. Make sure if you do this job yourself that you take the motor to the parts store so that they can match it up. The guy at the store told our maintance man if it didn't require the bolt holes in the motor housing it would have been $100.00 cheaper.