A bit old thread but I'm having the same kind of sounds.
I've been traking source of the sound down for a couple of days now because its driving me nuts.

Klonk klonk...from the pillari. Really annoying. I've sorted out that its not coming from the seat belt. Its coming somewhere inside the pillar when accelerating, on small bumbs and when braking.
First thought it was the door sealings but I've sprayed silicone into them and it didn't help.
I could really use some help. I have not opened the pillar yet because I'm not sure how to...