If your car has a decent amount of modifications, you may want to avoid a stock type harness. Why cut up a new harness to install your ignition box, one wire alternator, aftermarket gauges, big stereo, electric fan, etc?
If you think the stock stuff is a waste, I would look around for street rod parts. Street rodders are always wiring from scratch, due to old 6 volt wiring or new fiberglass bodies.
I wired my dad's 39 chevy from scratch years ago...it's not too bad. Just do one system at a time. Starter/ignition, then headlights, tailights/brakes, dash, etc.
For new fuse panels, check our Centech, Watson's Streetworks, or Ron Francis Wireworks. They all sell kits and parts. My dad just bought a panel from Centech....$125 and very nice. They also make generic pigtails that connect to the steering column for turnsignals, etc.
Also, I personally don't care for the Painless "stock" type harnesses where everything is prewired to the fuse panel. I think that would be a pain at the start of the installation. A panel alone let's you test, cut and route one wire at a time. This, to me, seems easier and neater, but I have never installed the stock type. Maybe I'm wrong.....
Regardless, I would just rewire the whole car. There's nothing worse that getting in your cool ride, everyone's watching, you turn the key, and hear "click, click". Humiliating!!!!!!
PS. My last advice would be if something doesn't work, check the ground. If it still doesn't work, recheck the ground. If it STILL doesn't work, have someone else check the ground. See where I'm going with this......good luck!