The 14 ga fuse link protects the alternator output wire which on a stock system is about 10 gage Fusible link should be 4 sizes smaller than the circuit it protects and about 6" long. The 16 gage link protects the wiring going inside the car. They are 2 seperate circuits. One feeding the battery, one drawing from it. Both wiring circuits use the starter relay lug as a power point out of convenience. What I did differently since I installed a larger alternator was to use marine grade 8 gage wire, with my own 12 gage fuse link. My alternator wire goes straight to the battery with a fuse link between it and the battery + terminal.
Pico wiring products sells fuse link wire in bulk length and you can put your own ring terminal ends on the fuse link wire and make your own.
The red and black wires going through fire wall both provide equal voltage power draw going into the car. It's not one or the other. Think of it like a stream with a Y and equally sized tributaries branching off, the water will flow an equal amount through both tributaries.
