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I have been reading the various issues discussed here and I must comment on the amazing knowledge base of the contributors of this form. I feel very fortunate to have this resource available.
I have a 2003 F350 6.0L automatic, and when I drive through puddles (not deep) a grinding noise develops, and a definite vibration is felt on the floor (both sides). This lasts for a few minutes and then subsides, while I am moving if I place the transmission in neutral the noise/vibration still takes place. If I park before the noise goes away and shut the vehicle off, there is a “clunk” at shut down.
I hope I have described this well enough for someone to give some guidance on what I should be looking for.