I am not sure what you mean by the strut clunking around ? Bad wheel bearing would not clunk...they would make noise when you the wheels are moving at driving speeds and perhaps have a little play if you push the car side to side when it is on the ground. The boot cover is a little cheap runner part that would move if the wind blew it...something is wrong with your struts it sounds like...how many miles are on your car ? Are the struts original ? I have yet to replace mine, but the original stuts (140,000K) are shot and they make all kinds of noise when I drive over bumb CLUNK CLUNK...??? Did you check the ball joints, control arms, etc...you can use a bar to pry on all these parts to look for any week points.
Some links:
http://www.clarks-garage.com/pdf-manual/susp-02.pdf
http://www.clarks-garage.com/pdf-manual/susp-10.pdf
http://www.clarks-garage.com/pdf-manual/susp-15.pdf
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1990-Porsche 944 S2 Project Hair Loss
2001-Saab 9-5 BSR Best car I have owned
2008-BMW 328i (Just another beamer)