Do i plug them together, or cap em off once I've removed the gps?
no, no, no.....
that is a silly question, but NO...
just unplug the 2 connections, and leave them lay, or wrap them in tape if you wish... think about it... you have 2 12v wires there, one is Pos+ one is Neg-.... pluging them together is like connecting a wire between both posts on a battery.. you will burn the bike down.
I really hope you read this before you even do what you were thinking, .. and, I can't fathom thinking that at all anyways.. but... people with out .... do .. odd things....
And, if you did connect them together, and nothing "happened"... and thought, "ok, cool"...(which with the bike Off, would be normal) and then, turn the bike on, and hit the start switch, energizing that circuit.... "Puffff"" and the "magic smoke" is released from the wire...