Sure - or you can just tape over the bare spots.
Make sure that the harness you got is NOT from an 01. The 01 harness is different from all newer ones; 02-05 are interchangeable.
And, welcome to the forum!
'01 660 Raptor, Burgard +2+1 arms, YFZ Shocks, LSR anti-vibe, CTR pipe, jetted, K&N
'01 Polaris Scrambler 400, K&N
'02 Honda 400ex, Big Gun pipe, jetted, K&N, Lonestar +2 A-arms, Lonestar anti-vibe
'04 Suzuki LTZ400
'16 RZR XP4 1000 Turbo