The diagram is quite plain... so let me make a suggestion that may help, and it's cheap to do.
Get yourself a piece of plywood (4'X8'works great). Then cover it with butcher paper that you can write on.
Now completely remove the wiring harness.
Attach the fuse box onto the plywood and start separating the wires into circuits that can be stretched out on the plywood.
You then start affixing the wiring to the plywood and labeling on the paper what the circuit is for.
It's an easy way to see how the wiring lays out, and to where....
It's like following a road map. In fact, if you look at a painless wiring diagram you'll see this type of process used.
When you've got the harness termination points identified you can then tie up the harness into a loom, and cover with plastic sheathing to make it dressed.
Also, Moses Ludel's The Jeep CJ Rebuilders Manual, 1972 - 1986 has a good diagram of the CJ5 (1972) wiring harness. It would go a long way in helping you to understand the layout, what goes where, what plugs into what...
Trust me... it's not as complicated as it seems.