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I replaced all struts with Monroe OESpectrum (refills) 2 years ago on my '04.
Right away, from just backing out of my driveway, the driver's rear made a clunking noise. I took it apart to find out the rod wasn't properly indexed to the mount (installer error- me). That fixed it for a while. It gradually came back. I hardly use the car, so didn't notice or much care.
This spring after coming out of storage it was almost undriveable, irritating to listen to the clunking, ever-persistent. I drove over a nasty set of RR tracks which really jarred something loose in a big way. I took it off the road.
I finally just now dealt with it. I took the assembly apart again to find everything was 100 percent correct. I put it back together only to find that the noise was slightly worse. At this point I was trying to see if I could warranty it out for a new one (send it back to RA?).
On their website http://www.monroe.com/en-US/shocks-101/faq/#faq9it it said clunking could be due to stretch of the stud. So, as a Hail Mary act, I put a washer under the mounting bolts and amazingly, that fixed it. Back to that nasty set of RR tracks and the noise came back, but went away after a few miles (studs relaxing after being stretched?). So yes, the next step is new upper strut mounts, or just live with it because it's tolerable to drive now.
I can't imagine the mounting studs stretched causing noise, but there you have it. I wonder if anyone has experienced "stretch." As a side note, I never torqued down anything so again user error maybe is involved, but still find it hard to believe the studs are that weak. Also, looking at the pic (before I put the bolts on of course) maybe I'm going crazy, but why are the studs so long?