Do you mean the two nuts holding a knurled plate and a slotted bracket together? Careful with those! They connect the main mechanic to the A-pillar latch. If they are loose the latch may fail to open/close, and if you tighten then in the wrong position you'll bend the actuating lever and will have a relatively big repair in hands.Then, apart from the clunks, I was also getting squeaks/rattles from the right C pillar. I saw the white 'marks' by the pen were not lining up. I got my 13mm socket out and tightened the nuts, the squeak/rattle is gone. The nuts were not even finger tight.
By the "black plastic spacer block" you probably mean the black painted aluminum wedge screwed to each side of the C-Segment. These you can untighten with the C-Segment over the M-Segment (2x Torx 30 screw), being careful not to scratch your beautiful black paint, and remove one shim from the side the noise comes from to add some tension to the system and prevent it from moving from side to side. This assuming there is one shim to be removed, as many Eos leave the factory with no shims at all.