It seems that maybe the wrong set of plug wires may have been installed...angled boots vs. straight boots or vice-versa. Your headers may require the opposite boots of what was installed. Maybe they need to be routed differently...tough to say without actually seeing it.
You can buy plug wires with high heat boots and there are also additional protective boots available to fit over the wires to help protect them.
Your application may require a different spark plug...the same heat range but a shorter ceramic for header use.
It doesn't sound like you have a serious problem, just the right routing of the wires or a different boot or spark plug application.