I think that my headers are effecting my engine....when I first start the car it runs (for lack of a better word)normal .But after it runs a little it starts running roughly.....I think this is due to the heat of the headers..Am I on the right track and will boot insulators help reduce or solve my problem . Thanks. Rick

Had headers on several cars and never encountered the problem...just make sure you have good quality plug wires.

I agree...your plug wires may be breaking down under heat.  There could also be cracks or pinholes in a wire that is allowing the spark to escape to ground.