I just wrote this up to answer another post, so I thought I'd add it here......
It really is simple.
Lay out the harness. it should be rolled up in sections....front/engine, dash, rear. Go through the wires and bundle all the wires that go to the same spot (coil, A/C, electric choke, alternator to engine. Front lights, signals, marker lights to front core support. Brake lights, signals, markers, license plate lights....fuel sender if you have moved the tank to the back.) Guages and switches to left side, radio and lighter to center, heat A/C to right side. Think about any accessories, changes, deletions, additions and make notes to follow.
Find a mounting spot for the fuse block....make shure it is easily accessable so when a fuse blows at night in the rain, you can change it.
Mount the fuse block, pull wires ....ALLWAYS through a grommet..light bundle through firewall to core support , engine bundle through firewall and to engine, rear harness through firewall and down behind inner fender, along frame to rear. Make shure no wires can move and chafe or touch a heat source. Pull dash wires and stick into respective holes.
Route bundles along fenders like factory, or under inner fenders for custom hidden wires. Plan where wires will route over to engine.
Start making connections after all bundles are located where they are going. I prefer to take the plastic off crimp terminals, crimp and solder terminals, then heat shrink.
Zip ties are your friend. Use plenty of them to bundle wires together. When you are all done, put final zip ties around harness, then cut all the others off to make a nice clean install.