I take my limited electrical knowledge for granted so I have to be careful when suggesting things. You might take a small 12 volt bulb or test light and extend the wires from your fuse holder. Placing the bulb where it is visible. This could be done by soldering the wires to a bad fuse and installing it.. You probably have a few by now anyways. . Then start disconnecting things. When the bulb extinguishes you have your shorted area indicated. Just keep moving along that line and disconnecting further along until you get to it. Of course re connecting what is behind to illuminate the bulb as you proceed. Should work out and pretty straightforward. If nothing else it will really tend to localise the problem.
Another option is to use a small meter. It will indicate you are grounded until you separate the shorted item.