When my '06 FXD (stock TC88, 17K miles) warms up, I can hear a knocking/pecking/clattering behind the stock air cleaner assembly. It is loud enough that I can hear it when I'm sitting on the bike, and when I try to find it, it is loudest in the air cleaner assembly area. Any suggestions? Thank you.

 

Those kinda sounds don't always come from where you think they are coming from.
The two most common area's on your bike to check are the tank bolts (tighten both ends with 2 wrenches) and the gas cap. (try pushing n it when you hear the noise)

and the obvious...check your A/C bolts

 

There is a sensor for the Euro Harleys that the USA models don't use - it snaps to the back of the A/C. Check to see if yours may have come loose and is just hanging there, rattling around.
~

 

Balingwire, have you had the timing chain tensioners checked? Had to replace mine at 20,000. Had a friend that had his fail at 28,000.