I really had no issues at all.
Working in the Auto industry for the last 25 years helped me get
my head around it...
The one reason that I use the same color wires as the factory is that without thought we should want to put like colored wires together and if you do you have hooked up the wiring correctly when you install my harness.
We also think from left to right so again without thought we should want to place the # 1 wire on the left plug and so forth; but even if you thought from right to left and installed as such it still works just the same.... Thus making the harness just about a foolproof install that one would have to try very hard to install wrong ....
As to the left over red wire tape it up for a rainy day; as you can use it to switch a relay with the key to turn something else on/off.
The remaining black with yellow stripe is a ground wire; keep it out of the way or re-ground it to help strengthen the entire ground system on the bike.