Mine used to do the EXACT same thing. If I shifted hard, or at high rpms, it would clunk just like you are saying, kinda feel it in your seat and feet at the same time. It ended up being the pinion bearing went out, and allowed the pinion shaft to slide back and forth, and have a crap load of slop in it. I just tightened the loose nut for about 200 miles till I got paid, fixed it for a while, but then it finally went out bad in town. It would lock up if I came to a stop. It was horrible, possibly deadly if it happened on the freeway. When I finally put a new third in, it all went away. So I say definetly pull your third out and check it.
