I've done it both ways - coil excess wire and customize the length.
It is odd how they do not provide enough wire to run across the firewall, and precisely too much to run across the radiator.
Since customizing the length makes looming the spliced sections awkward (it is a vinyl sheath, not split) you're faced with taping and relooming the wire. This is all doable but at this point you might be tempted to make your own custom fusebox that has relays for headlights and room for expansion.
In my mind the big advantage of the koito kit is it's plug and play simplicity. Use Matt's brackets to put the fuses near the battery and the relays near the RH headlight. Route the wire along the front cross-member and under the radiator. This is stock for 40s up to a certain year. Coil the excess and zip-tie the coils out of the way, near the headlights and battery.
If you decide you want to have a more tightly integrated custom setup then consider building an Ultimate Fusebox:
Schematics and Technical Design Details
Here are the schematics for the FJ60, FJ62 and FJ40. When I originally upgraded the headlights in my FJ62, I built a wire harness from a kit. It was built around three discreet relays mounted behind the air cleaner and wires that went across the bottom of the radiator to get to the headlights on the drivers side. I was never really happy with how it turned out. It worked OK, but I thought I could do better. I scoured the Internet looking for a better relay package and came across the Bussmann RTMR relay module. It is designed and rated...