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Okay, stupid question, but I have dissasembled my 01 struts, while Im waiting for my tein SS's to come in. However, I wasn't thinking I needed to mark them, because I assumed that was only if I was re-using the stock strut, is this correct, or should I have marked them. Does the upper mounts fit into the frame any which way, like my Hayame's or am i screwed if I didn't mark them??????

 
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There is a specific way they fit as the holes aren't symmetrical. No you don't need to index.

 
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once you assemble them, just rotate the mount until it matches up, i think its marked with an arrow etched into it that denotes which corner goes toward the inner side of the car.

 
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Arrow points straight forward. You don't need to index coilover springs.