I had this very same issue, i went to kmart who said it needed a shim adjustment on the valves but that i should take it to toyota as they didnt have the gear to do it,
so to toyota i went.
They looked at it and said it was a high finger on clutch.
so since it was a 9 month old hd clutch kmart put in i went to them and claimed a warrenty repair.
While all the gear box was out the kmart mech also looked at the clutch fork, this turned out to b the problem, he did his research with toyota and found out the clutch fork had been re designed 3 times for the 2006 sr5 due to "issues" . Toyota declined to elaborate.
Anyway, it turns out the knuckle that joins onto the clutch fork had come loose which created the rattle, the rattle then went away when i placed my foot on the clutch ever so slightly.
Kmart gave me a new hd clutch anyway as well as paying the $220 for the clutch fork and knuckle and free labour of course and i can happily say after 4 weeks im still rattle free.
After seeing the clutch fork and knuckle the took out im certain that was the issue and not the clutch. score to get a new one though
The rattle happened at idle, when driving at high and low speeds, drove me crazy!
Hope this helps