Hi Ianc,
Nice post and pics. I want to do this suspension mod too. I would have chose the same parts Koni's & Eibachs.
As for your clonking noise... I dunno. I guess since otehr people have this noise... I would disconnect one end of your sway bar link and take it for a spin. See IF it still makes that noise? I guess you checked your bar bushings to make sure they are all good and tight. ?
I know in the past... from other car makes(VWs)... I have heard a loud popping noise under really bad broken road surfaces... esp when your on said road and brake really hard... it turned out to be dirt on the subframe where it mates to the body. Or sometimes just loose subframe bolts. Try checking your subframe bolts - to make sure they are good and tight.