Anyone know a good product to clean but not damage headers?

what exactly do you mean? clean up?

so not stock right? I would say take em and pop teh hood at the local car wash and cover coils or dstr. with grocery bag and blast em with the spray.. select engine clean on the spray.

are they long tubes? ?

What year stang is this? After a certain year (not sure) ,Ford changed the quality of the pipe material to cheaper steel. I know you said it's not factory but this will narrow it down. Can you take a pic and submit it here?

Any rust on them? Chalky white residue? Don't use any type of acidic cleaners. They may do more harm than good. They may bring them to look like new, and then later the pipes will start corroding from the chemical that was used. If there is white chalky residue on them, chances are they are alumnized pipes. Slight rust and they may be stainless. I know 94 - 98 models had stainless pipes from the factory. Stainless cleans up pretty easily. Alumnized doesn't. It's hard to say without a pic.