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I just spend the day putting on Bilstein on m 04 the front went fine with dust boot on top just like the old one. But on the rear they would only go on upside down with dust boot on bottom.
They are designed to be installed boot down. The ends are about 3/8" different in width. If you try to install them BOOT UP you will need to bend open the upper mount, thats the hard part. Then crank the lower bolt to squish the lower bracket closed.
This may be the other way around i cant remember
The reason for boot down is to lessen the total weight of the moving mass, The entire rearend assembley.
Some will say it doens't matter and it indeed, may not. I'm just answering the question.