I have this whirling noise which gets very pronounced at speeds of 50-70mph.
I have changed out the wheel bearings already. Bought new tires all around had the car realigned. My mechanic thinks the differential may be going bad. He did take a look at the fluid and said there are small particles in it but it was pretty clear still. At 85 mph and above.. the noise is quieter.
Any advice?

 

All 4.0s have the Ford 5R55N trans, which uses cheap fluid. See stickies for a HowTo.
I'm not convinced it's the trans making the noise, though.

 

Not really a noise reported for transmissions. But yes you should change the fluid and filter. Change the rear end fluid too. It might be low as no one ever checks it.

As JagV8 said you don't have a ZF transmission. You have a dead common 5 speed Ford transmission. This is a plus as it's been installed in millions of Fords and is very well known in the aftermarket. Much cheaper to work on and much cheaper parts including the fluid.

At speed (50-70 mph) shift into neutral and see if the noise changes.
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That whirring noise could be a bunch of different things. One thing I learned a long time ago is road condition and tires will make some gawd awefull scary noises!

There is a stretch of road between me and work that my tires sound like a jet engine on it. It last for a mile or so and then back to its normal quiet ride.