Get this. I have the same clicking noise (the dealer "fixed it" by taking the dash out and "insulating" things, but the fix only lasted a week or so). It starts when:
a. It's cold outside, and:
b. The car hasn't completely warmed up.
But it doesn't do it on the highway - only at around-town speeds.
So let's see: doesn't do it when the engine is hot (warm weather or warmed up in cold weather), driving at highway speeds, or engine is very cold.
Under the hood is an insulating pad. I noticed it was kind of loose, so in frustration I took a wadded-up Coke can and stuffed in under the pad - in front of the driver-side. Clicking noise is gone.
Hmmm.....
I have to say my 2006 FX35 has lots of squeaks and noises. Like there's lots of body flexing going in & out of the driveway, etc. The front windows squeak in their tracks, but an occasional shot of silicone spray fixes it.
FYI -