I would endorse the 'clear the boot out' theory. I get an occasional clunk from the back, but it's definitely from within the boot.
The clicking sounds like noisy injectors. I owned a 156 2.4 JTD for 10 years and 95K miles from new and it's still going well with a new owner. The Brera 2.4 JTDm has done about 25K miles and it looks like it will be similar experience. They can both clatter a bit under acceleration in the way you describe, although premium diesel and/or injector cleaner can quieten things down a bit. You can either shove snake-oil in the fuel tank or, provided it's not causing other problems like excessive smoke or fuel consumption, just put up with it.