There are 2 doors on your furnace, the top goes to the heating element and the circuit board. These covers don't swing open, they are lift and pull covers.(I am guessing that you already know this but for other readers who may not know this will be helpful).You will find the wiring diagram on the inside cover. There should be a 3A fuse on the board beside the electrical connections. If it's a newer unit it will look like an automotive fuse, older units have Buss fuses.

It should take more than a minor short to fry the transformer but it's possible. Also try to ring out the lines from/to each point, you may still have a short or open in the wire somewhere.Maybe in the wall where it leaves/enters the house.

Good luck.

Please post your findings.