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What RPM are you shifting into 5th gear at, and what RPM does it drop to after shifting? Does the sound go away at higher RPM's in 5th gear?
My father had a small chevy truck with a 4 banger and he used to shift that thing into 5th gear at about 35 mph to save gas. It would rattle and make all sorts of noise because 5th gear was not made to handle that low of speed. The transmission lasted about 25,000 miles.
Not saying that you are shifting that low, but you might be shifting just a little too low for your differential ratio. if there is no rattle at higher RPM's n 5th, that might explain the rattle.
If not, then I am thinking that it might be the linkage rubbing on something as there is not a lot of room in the tunnel and so far nothing has shown up on internal examination of the transmission.
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