I'm sure you already thought of checking the battery to see if the fan pulled too much power from it while it was running and the truck wasn't... I have the same fan on my 92. Mine shorted out once too and my truck overheated and burnt a rod bearing...
If the battery is good, and it's just clicking after shorting out a fuse and you checked the connections at the battery and the starter, obviously it must have burnt another wire somewhere. Sorry to state the obvious.
Where did it blow the fuse at? Was it the in-line fuse between the positive battery terminal and the fan control, or was it a fuse somewhere else?
Sounds like you have the fan setup to run off the thermostat and if it came on when the truck was hot and went off after it cooled it off you must have it working right.
I would start by identifying which fuse shorted, check the battery and start narrowing it down from there. If the starter selinoid is good and the started clicks when you turn the key, if it is getting enough voltage it should at least turn the motor over...
