I'd try checking the wiring in the trunk as this is the most likely area where wiring can be damaged.
Next I'd try removing the bulbs for the stop and running lights, fit a new fuse and see if it blows (making sure the fuse is the correct rating for the circuit) first by pressing the brake pedal and then by turning on the lights. With the bulbs removed, there should be no current flowing in the circuits unless a wire is shorting to ground.
To narrow it down further, you could trace the wires from the lights not working back to the fusebox terminals or switches, disconnect them and then reconnect them in turn until the fuse blows.
Another alternative is to use an ohm meter with the power off in the circuit being tested (battery disconnected) and see which bulb terminal/contact is shorting to ground, i.e. meter reading 0 ohms.
There is also a type of tester available afaik which can identify if a wire is live or shorted to ground but I've no experience of this tester.
AL.