I know it may sound weird, but I had the same problem and it is pretty common. The stock headers on the v6 Mustangs have weld issues. I only could hear mine clicking when my engine was under mild stress...i.e. a/c turned on, accelerating, etc. Check the headers for leaks around the ears that bolt to the block. You can buy new stock headers, but it'll happen again. I just went to a muffler shop and had them reinforce the welds. It works great now! No more clicking. I've told this to several people on the road that I can hear. The next time I see them, they always thank me. Good luck!