I've been having the same issue, I'm pretty sure it's the input bearing, as stated.
I just don't feel like dropping the trans yet, as I plan on doing a lot of work while it is (IMSB, RMS, clutch).
There's probably some other component (internal to the transmission) that would be good to replace while I'm in there, but I haven't done enough research.
Clutch-out-in-neutral noise is pretty indicative of input bearing noise, though.
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'97 - Silver (rebuilt/stripping)
'99 - Black (rebuilt/sold)
'01 S - Rainforest Green (daily)
'03 S - Orient Red (sold)
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