I suggest you find a good reference on automotive electronics. It will serve you well now and in the future.

An alternator cannot "overcharge" unless the regulator is not functioning correctly. An alternator also does not put out more amperage than is required from the system. I.e if your max load your truck could ever possibly draw is 65amps, your 200amp alternator will never put out more than 65amps.

In general, a vehicle draws current from the battery, with the alternator providing the juice to keep the battery charged and to provide current in excess of what the battery can provide for peak draws (winches, stereo, lights, ect). It is not quite a flow-through system, but for the purposes of this discussion, consider it as such.

In your case, you should upgrade whatever the heavy wire from the alternator is. This should be on some sort of ring terminal on the back of the alternator. If it goes through the fusible link, so be it. I don't feel like looking up the wiring diagram right now, that is your job. :-) But, it should go to either some sort of power distribution block, the battery or a fuse box. In general, you don't really need to put a fuse on the charging wire for the alternator, but there should be fuses between it and anything that requires amperage. I would suspect the fusible links are for things like the headlights, which need considerable amperage, not on the incoming wire from the alternator.

Good Luck,
Michael