I believe the Samurai alternator is rated at 35A. With stock wiring, all the alternator charge current flows through the fusible link. Also, all the electrical system current flows through the link, from the battery and in the other direction, when the alternator is not running (it's the way it's wired, and not a defect).
Fusible links are VERY slow-blow fuses. On my rig, I would prefer to replace it with the OEM part, or near equivalent. But, if I had to use a fuse instead, I'd use a 40A MAXI
fuse. They are a lot slower than the smaller types. You are protecting the vehicle wiring, which is a slow-blow application. MAXI fuses have replaced fusible links in many late-model vehicles (although they do not have the same performance characteristics).
If your battery is not fully charged before you begin, the full alternator charge current flows into the discharged battery, though the fusible link, as soon as you start, which is what may be blowing your fusible link/fuse.
High-current alternator upgrades REQUIRE a separate, #6 (or larger) alternator charge wire directly to the battery to prevent blowing the OEM fusible link. The existing OEM alternator charge wire is simply taped off and no longer used. The OEM fusible link protects your vehicle's wiring. One electrical fire could ruin your whole day.
Edit: Added a Fusible Link Color & Ratings chart at: https://www.suzuki-forums.com/gallery..._Link_Info.gif
. The Samurai uses the green 0.5 square mm link.