Ok, I think what's happening is that it is cooling the furnace to where the blower sensor sees that it's too cold, and shuts it off. However, maybe the sensor is bad, or improperly adjusted. You could try adjusting it to colder temps, but if you're really over on the blower your efficiency will go down.
Is the motor configurable for speed? IE, does it have a fuckload of wires coming out of it, or just two?
Try obstructing the return register about half-way with some plastic or something. Try to get it so the flow is what it used to be, and see what happens. DO NOT let it keep running that way forever, you'll stress the motor and kill it, but it will give some answers.