When you click on links to various merchants on this site and make a purchase, this can result in this site earning a commission. Affiliate programs and affiliations include, but are not limited to, the eBay Partner Network.
No, it won't matter which one you use. But to keep it simple just use the orange/white. Connect the orange white on the Metra harness to the orange/white on the deck harness.
No it's not needed for an aftermarket deck. I figured about the same, it must be something to do with OBD2 and/or the PCI bus. It's a good idea to tape it off or zip tie it back to the radio harness so it does not short out against the chassis of the new deck.
The blue/white on the JVC deck will connect to the remote on for your Kicker amp. The blue/white on the Metra harness does not get connected to anything. If you still had the factory Infinity amp in the system you would also connect the blue/white on the Metra harness to the blue/white on the JVC so it would turn on the factory amp and the Kicker sub amp.