I had a similar issue a few months ago. Once in a while, usually when I hit a bump I'd see the alternator gauge move quite a bit. Then one day driving on the dirt road to the house the 60 amp fuse blew. I popped in a new one and it worked on for about 5 minutes then it blew. We towed the X home and I started digging into wires..
Short story, a shorted wire under the dash..
Long story..
I did some digging and found that the 60 Amp ignition fuse powers the ignition switch and things that come off of it. At which point I threw a new ignition switch on it. Not the key thing, but the thing that actually controls the electricity that is on the top of the steering column. That didn't fix it.. Then I put a new fuse in and it didn't blow. I then started to push/pull twist etc wires under the dash. Basically any of the wires to or from the ignition switch and viola.. I moved just right and it fuse blew. A little more digging and I found that the PO had hooked into a switched power wire right off the ignition switch and they used a wire nut which had come loose. There was bare wire that would touch metal when it moved just right...
So, grab a wiring diagram and follow the wire to and from the ignition switch. If you still can't find it you may have to go as far as cutting some of the output wires off the ignition switch so you know what branch the issue is on to narrow down what your looking for.
~Mark