Absolutely use original colors! No offense here (I ain't no electrical guru) but you ask a question about replacing wires. Which indicates (again no offense) electrical isn't your strong suit. Now you want all the wires all one(maybe 2 or 3 colors)???
Can you imagine 6 months down the road tracking down a wiring problem? Then asking for help on here?
Screw that do the proper colors or go buy some markers.
Again no offense
That's up to you to do it however you want to, but doing it with the factory colors might make it easier now and easier down the road if you have an issue.