Last week after I drove my X-90 home from work (90 miles |removethispart|@ 90 MPH) My transmission was whining

. It sounds like a bearing going bad. This same thing hapned to my Kick at 150K but it started quiet and took a month to get loud.
The only time it does NOT make the noise is with the clutch pushed in and the shifter out of gear. Input shaft bearing

I'm going to pull it this weekend when I'm installing my Calmini 2" lift on the X. Has anyone re-built their trans after having this problem? If so what was worn out? After having the same thing seem to fail in both my Kick and my X, and hearing of this same thing on a couple of others, I would think it would be a bearing wearing out?