if you want to risk burning up the wire harness then by all means throw a larger fuse in it. (of course i'm not being serious so dont try this)

But....
If you want to find the problem with no risk to damaging the truck further then the correct course of action would be to backprobe the system starting at the fuse and locate the shorted wire or component. Performing an OHM check sometimes is not enough, you might have to do a resistance check on the circuits in question instead which requires more time but can be more effective in locating your problem. This may also require using the wiggle test, moving the wiring around with leads connected to try and duplicate the shorted condition.
A wiring diagram would be extremely helpful to keep you from doing any unnecessary probing in areas unrelated.
From the sounds of it this problem may be wiring related since it only does it while its running, a chaffed wire moving around rubbing on the truck somewhere can wreak havok on troubleshooting effectively and will drive you nuts till you find it.

Good luck