I have an older Rheem furnace. I had a tech. out two weeks ago and he replaced the blower, circuit board, limit switch, and capacitor. One week ago the transformer went, I replaced that with a used one and it blew that one immediately. Went out today and bought a new one (put that in along with two 3amp fuses to keep the transformer from going). Now, the furnace makes one full cycle but then blows the fuses when the blower shuts off at the end of the cycle.

You will have to use an electric meter to track down the short circuit that is causing the problem. There is no way we can do that here.