I'm wondering whether the takeoff was actually from 04L (the usual takeoff RWY at EWR) and the debris was only found on 11 (which crosses 04L at its far end).
Listen to the audio from oliver2002's blog link above:
http://www.wandr.me/Audio/UA96.mp3
UA 96 is cleared for takeoff on runway 11. They say they have a blown tire, sounds to me like they say they are declaring an emergency for a lost engine on the first call to departure control, and later say they have two good engines, not two 'red' engines as reported in the Aviation Herald link.
Not sure what two 'red' engines means unless it's an Ozzie term or something.
They weren't holding with an engine shut down as speculated earlier from what I hear on the recording.