Even though the fans and fuel pump are relayed the charging current still has to go through 2 bulkhead connectors and the ammeter, the bulkheads will not take this abuse long term. The easy solution is to run at least a 10 gauge wire and 30 amp fuse from the alternator post to the battery, 6ga and a 60 amp would be better. It would be wise to add another ground from the battery to the alternator or block as well. This takes the heavy charge current off of the old wires and bulkhead connectors. You are having problems with the fuse link and blue wire because they are overloaded, a jumper will solve this. The stock circuit runs a black wire from the alternator to a bulkhead,then to the ammeter, then turns red and tees for the headlights, then red to another bulkhead, then turns blue and end in a fuse link at the starter relay. A simple 10ga wire and 30 amp fuse eliminates the heavy load on all those connections, try it , I have been doing it for 30 years now, might save you a fire.