So, this is a simple wiring job that I did on a motor that I'm not going to use. It's not perfect, but it'll do for the how-to.
These are the tools and supplies you will need. Knife, tweezers, drill and whatnot. The motor and distributor, and wires. The thin blue wire will be the ignition wire, the thick black wire (sold as coolant hose) will be used to make the boots for the sparkplugs and the distributor.
The sparkplugs are easy to find on this motor (called out in the photo with sharpie). You could either drill these out, or use them to hold the boot. They are short on this block, so I am going to slice them off and drill them out. On my 787B, I just slipped the coolant hose "boot" over the nub "sparkplug."
Drilling.
I put the distributor in place and then marked a length of wire so it would run from the distributor to the furthest hole. Over estimate this distance, and trim later. Wire is cheap, and it's a pain in the butt to redo it many times.
The coolant hose has copper wire inside the insulation. It will have to come out. To get it out,
carefully cut through
just the insulation. Then, carefully again, use the knife blade to draw the copper wiring out and discard the copper.
Cut short lengthes of the insulation of the coolant hose, and then slide them over the wire. My drilling into the block wasn't big enough for the boot, but it was for the wire. That's why it sticks out a little further. Usually, I make the hole big enough. Oops.
Put a little CA (superglue) on the end, slide them into place. Look, a wire and sparkplug boot!
Repeat for the distributor. There is an extra bit of boot in the center (for 5 boots total in this case, arranged like the 5 dots on a domino) for the coil, that will be added when the engine is installed, and wired to the distributor.
I hope this helps. This was only 4 wires, but the principles hold the same. On my 787B, there were really big boots, so what I did was slip an even larger peice of wire (actually, vinyl tubing) over the coolant hose, just like I put the coolant hose over the wire. It's really quite simple. A lot of times, you can slip the "boots" over little molded on nubs, and that makes the work a little easier. For cars like a Civic, where there's a cover over the sparkplugs, all you have to do is the distributor. Then you can just cut a hole at one end of the valve cover, under the sparkplug wire cover, and slip them in. No bother over boots on that end. There are also pre-wired distrubutors available, but these are usually for V8s. You could, I imagine, cut off 4 wires and use it on a 4 banger, but it wouldn't look right on a 6cyl.
And as with any how-to, tip or trick: Feel free to experiment with any of these steps and do it your own way.