I had a similar clunking/rattle on the right rear when I got my car..... I checked everything and never could figure it out. Then, when cleaning and installing new rear speakers I had the back seat out and discovered that the plastic cap that covers the upper shock mount was off and laying under the seat. I don't know if it was the cover clunking around or just the noise let in through the uncapped hole but the clunking is now gone. Maybe it will be something that easy. Good luck.

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1985 300D Turbo ~225k
2000 F350 (Powerstroke) 4X4, SWB, CC, SRW, 6spd ~148k
1999 International 4900, DT466e (250hp/660 ft/lbs), Allison MD3060 ~73k