you might want to use a larger wire with a fusible link from the alternator and connect it at the starter on the same lug that the main battery cable connects to.
The original wire is fairly small gauge. The later model alternator will be a higher amperage and may overload the existing wire.
You will need to keep the wire from the battery to the terminal on the fender as this wire feeds thru to the fuse block and powers everything inside the cab along with the lights, switch, turn signals, accessories, etc...
The factory 5.3 has a fusible link from the alternator to a little red junction box that connects it to the positive battery cable.
Keep in mind, there are other ways to do it....this is just one way.
Essentially what you're looking to do is connect the alternator output to the + side battery in some way (safely).
Here you can see the fusible link as connected to the battery cable on a 5.3 taken from a 2001 Tahoe