The cleanest setups I have seen simply use the 5.0 style valve cover bolts that have the stud on top of them about 1" long.  Then they make plug wire clips that slip onto them having 2, 3, or 4 wire positions.  Those make a very clean installation if you cut the wires the right length and you are using factory parts.

I would run my wires like that, but all the valve covers I own have the steel clip on them to hold the wires up on top.  If I figure out how to mill the slots and lose those clips, I would do mine that way.

You can walk down the old Ford row at any wrecking yard with a 7/16" deep socket and come back with enough of those studded valve cover bolts to do several cars.

Here is how I did mine.  I bought the wire holders from MSD and then made my own brackets. 

Terry - I like the addition of the spacers ... question for you, how long are the spacers you used and where did you get them?

Zip ties here too

+1 on the zip ties.
I bought a bag of 1000 zip ties at a car show/ swap meet a few years back and I use them for the spark plug wires.  You will go through a couple dozen of them, but when you replace the wires you can throw them away. Even after several years, they still look the same and don't seem to break down from the heat.

BobN