Boss, the fuse will protect the alternator, the wiring and the battery in case something fails.
Fuses or fuse-able links are used in cars and tractors in all modern applications, if someone is going to upgrade to an alternator I think it's a good idea for protection. I have included the wiring diagram for my Kubota to show how its used between the alternator and the battery.
On Bus Driver's comment about the size of the fuse:
We've been talking about Delco 10 63 Amp, Hitachi 14321 35 amp and the Hitachi 14255 50 amp alternators. On Farmall tractors about the highest RPM is 1600 (this is where the drawbar horsepower tests are done) and with a 1.92:1 ratio on the crank to alternator pulley, the alternator rpms is about 3000. At 3000, these alternators will output approximately 60% of their rated output At 3000 rpms, the Delco 10 is 38 amps, Hitachi 14231 is 21 amps and the Hitachi 14255 is 30 amps. So I think a 30-40 amp fuse is about right for a Farmall tractor using on of these alternators. If it blows for no reason, I'd replace it with the next higher fuse.
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