I have the SD headers as well with factory ac delco wires... I'm thinking bout going with msd 90° angle wires...
pull the wire back so the boot is pulled back, then clip it in the clip. if need be use a zip tie to hold it back. mine are advance auto wires. maybe they are a shorter boot? not sure.
I have mine with the clip on valve cover but the end of the boot hits the tube on my header