Is the clearance wire for all the side lights not part of the wiring harness
I got with the new light kit?

They just splice in but you are correct, every splice is another point for
corrosion failure.
What I do is run a wire from the side light BACK to the tail light and connect
them all together with one crimp connector. Then put a dab of silicone on each
end of the connector to seal it. It takes a little extra time and wire but it
works for years.