Ok, the first step is a powerfull alt able to feed around 45 amps iddling as minimun as my opinion... no matter what you get on wiring or gauge! More is better, but AT LEAST a 45 amps iddiling alt
The fuse link is not really neded on alt side but on batt side. Why? On a short, the batt side is the only source able to keep feeding the fire. If you didn't have a batt running and just the alt, when you get a short, the engine will stall, because the short will suck put ALL the juice and alt won't be able to source it, so engine will die. Aside that, if engine is not running and get a short, the fuse link on alt side is out of the game, since is AFTER the main splice. The batt will keep sourcing the main splice.
So on the basics... yes, is just about a straight wire ( 8 or 10 gauge ) between alt and ammeter, then from ammeter to the starter relay/batt, with the fuse link on this leg.
THIS IS A SUGGESTION IDEA:
I would use a quick disconect link to be able to unplug these new paths just like you are able to discinect the bulkhead... just about versatility prefference. These are available up to 48" which allow to use a large section straight to the amm studs keeping the plug on engine side, and a short harness section with the other plug to splice there the wires up to alt and starter relay.
Be sure ammeter is in good conditions, tight studs to the internal shunt, same as BOTH isolators there and good.
NOW, if STOCK wires are still in working order, you don't need to remove them, not at least the alt one. Just mantenience. They will be safer now with the new alt and batt added paths.
If decide to keep both stock existant ones, need to take in mind need JUST one fuse link on red lines... splice both in the fuse link ( 14 gauge ) or simply remove just the stock red one for simplicity