Headlight relay system and Convertible top relay system recommendation

Sizes all fuses, breakers, etc. based on the weakest wire in the circuit. You seem to have a handle on how to wire distribution, so size each fuse or breaker for the circuits downstream. If you want to see what AMC did when they changed wiring strategies to something more like yours, I have a simplified version posted here: 1986 AMC Jeep SJ Charging and Ignition Wiring Diagram
The green ones are all 18 ga, and the yellow one 14 ga.
Links are 2 wire sizes smaller than the smallest wires in the circuit. Or at least smallest unfused wires in the circuit. You can see in the factory diagram the 14 ga fusible link connects to the 10 ga wire to the alternator. http://oljeep.com/gw/elec/86/86_FSJ_WiringDiagramPage2-1.gif

I can't tell you what the lengths ought to be, but if I remember where I saw it, I'll post up if no one else has. I want to say it was in a factory service manual, but even so, I don't know which one. Maybe the Chrysler Master Tech Bulletin on Wiring diagrams.