I'm not sure if this helps you, so feel free to ignore me, but...
I have built multiple project (car and motorcycle related), and when removing stock connectors (or having no harness to begin with) I've had great success with these weatherproof units:
LINK
You can use your existing wiring, or set them up with whatever colors work best for your application. They come in all sorts of configurations (2-wire, 3-wire, etc.) and they're cheap. My cafe build utilized a 5-pin for the entire rear lighting, which cleaned it up dramatically, whereas the headlight and front signals needed to be kept separate so I used one 3-pin and two 2-pin for those.
What's also nice is that, should you want to swap out a component, they're cheap enough that you don't need to cut/solder anything. Just use 1/2 of a connector on the new component and toss (or save) the other half.
side note: the link provided is just for one size. they have TONS of options.