My best guess would be something with the exhaust. I noticed that my car after a long drive sometimes when idling will make a clanking sound too but it's the exhaust hitting the suspension in one place, it's badly welded but it dosn't bother me. On the other hand, my dads acclaim clunks like no tomorrow because the honey comb in the catalyctic converter is loose, the hotter the exhaust gets the stranger noises it makes. It's all I can think of, I would not say it can be engien related cause engine you will hear from the beginning to the end, so it is most likely something that changes shape a bit once heated up, like exhaust.

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