If the funds are available for you, we highly suggest starting over with a fresh harness for exactly the reason you said. You can start fresh and cut off any excess wires you won't be using. The MotoGadget M-Unit is ideal for this. There are just a few things to consider:
If you are going to run the lithium-ion battery, it's important that the regulator and rectifier are lithium compatible. We do not carry a lithium reg/rec for this application, however, our vendor Rick's Motorsports does manufacturer an option (SKU 14-202H). You will want to also make sure you have some suppression wires in an attempt to eliminate any electrical interference. For the harness, you could start completely from scratch or an alternative would be the cable kit (SKU 19-0609) that will help tremendously with the installation. A common ignition switch used by many would be a two-position switch which you will be able to source elsewhere if you would like. The OEM/factory three-position switch can be used but the m-Unit does not have provisions for the third parking light position. So if you stick with your OEM, you can either wire it as a second-on position or cap those wires off so that they do not short out against the frame.
The M-unit will also have an integrated starter relay for the solenoid switch (up to 30A switching capacity) but, all starters with separate starter relays (e.g. Japanese models) must continue to be operated using the original starter relay. While the m.unit itself does not need a fuse, the implementation of the main vehicle fuse (maximum 40A) is mandatory, since the voltage regulator (connected to the battery via the main fuse) may malfunction and create a short circuit.
I hope this helps with the basic core components, for all other additional Motogadget items you can check out our selection here: https://www.dimecitycycles.com/search?q=motogadget
Again, this is a universal set up and not motorcycle-specific.
Thank you for your inquiry,