1) Buy an aftermarket, gas-tight battery box with a vent.
It's absolutely mandatory, both to properly restrain the battery and to vent the gases created by charging the battery via the alternator. Transplanted OEM hardware won't pass tech inspection. Furthermore, the concentration of hydrogen gas in your trunk will facilitate corrosion and could lead to disaster should the battery terminals be short circuited.

2) Your fuse needs to be inline between the battery and fuse box..

3) In order to replicate the OEM wiring harness, splice the two 4-gauge wires together at the battery terminal clamp. I did this when I relocated the battery on my GTi, just strip, braid and clamp.