I have a similar problem. However, on idle it stops. I can rev the engine all I want and it's smooth as butter, however, once I start moving/accelerating I get the click, or a clack as I like to put it. Funny thing is though, that after the car reached operating temps (5 minutes), the clicking goes away. I have no shifting issues, no gear grinding, etc etc. My clutch is nice and firm.
A month ago I exchanged my shot muffler's for a MAC catback system. I have MAC headers, however, my stock h-pipe is FORD made. I have a really good sneaking feeling the clicking I hear and I've heard it a couple of time when the car WAS idling is coming from the area where my cats are! I really think mine are shot and need to be replaced. Maybe when the installation of my catback system was being done, the h-pipe was removed and the element was somehow dislodged and now 4 weeks later I need new cats.
My click was a little louder originally, but has since quieted down a little which to me means they're disintigrating and blowing out the back piece by piece.
I'll be swapping those out sometime in September.
So far, I've not had any power loss issues or overheating due to clogging or congestion of the filter element in the pipes. I've checked my cats and headers in the dark after a long drive and they have not changed colour meaning to me the car's still breathing ok.
The good thing about a welded exhaust is you'll never have to contend with rattles due to joints coming undone, however, they suck to work around as you pretty much have to remove your rear wheels and springs to install them.