Wow!
First thing I thought of was something on the flex plate was bad, but you checked that.
If the tranny was acting up I would be suspicious. I've never heard a tranny make a noise like that, but it is an E4OD and some have had problems.
I associate E4OD problems with torque, I had a 94 F250 with a 460, with one and it was problematic. I have one in the Bronco and it's great.
I also might think water pump but the noise seems too far back.
I'm not helping, but boy, that sounds terrible!