I think squirrels do in fact get into the ducts of jeeps.
When I bought my TJ is had a fried heater fan speed resistor pack, when I went to replace that, which lives in the heater duct, I found that my entire heater duct was completely packed with hay and straw, and other materials that totally looked like a nest of some sort.
Is the noise only when you have the fan on? Does it change based on fan speed?
If not, then unfortunately, you're probably dealing with something transmission related, like a bad throwout bearing or pilot bearing.
I guess, all said, we're going to need more info about the noise, when/how it happens, etc.
