It is most definitely your manifold I've had a 99 and 00 mustang with ticking noises from the hood it's the ****ty exhaust header with horrible welds messing it up either take it off have it re welded or buy anew one I've done both a new header is around 70 bucks
I have a ticking, but it's a small hole in the exhaust system. It got welded good and went away, but I have a lot of BIG speed bumps in my complex and it messed up the welds again. At this point, I just deal with it and don't worry about it. With these speed bumps all you do is scrape scrape scrape.
Mine goes away too after the motor is warmed up, I thought is was the manifold. I plan on getting a set of headers when I get my exhaust done so Im not gonna worry about it now. Thanks for all the help everyone.
JVC Head Unit, 1000 Watt Pioneer Amp, Two 10" Pioneer Subs.