Thanks a lot Kenny. I took the 4runner yesterday to the mechanic and he told me they removed the driveshaft and that the yoke and u joints were worn out and needed replacing. I should probably call him and tell him about the rubber lining.
I was wondering if you ever figured out if it was the u joints or the bearings. I just got a 2000 4runner that my sister gave me and I'm having the same issues among others. Right when I hit 60 i begin to also hear a humming type of noise. Thought it was the tires so I replaced them but still...