The two most common mouse-rat entry points on any vehicle are the cabin air inlet, and cabin air outlet vent. For your 2008 JK, air enters at the cowl below the windshield, and exits via a flap-check (1-way valve) vent behind the spare tire.

Your 2008 doesn't have a cabin air filter (I made an adapter for mine), but even if it did a determined rodent can chew through one, as well as the plastic and rubber rear vent behind the spare tire.

On a related note: I'm just back from vacation on the East coast and helped one of my kids find and fix a rat entry issue with a Subaru BRZ. One of the two cabin air exhaust vents, which is designed same as the Jeep, was chewed out -- And by the amount of plastic chewed away this was a very big rat. We blocked off the half of the vent that was destroyed, and in one night it had chewed through the plastic and rubber for the other half of this vent. So now we blocked off both halves with thick rubber that was glued to what remained of the this plastic grille vent, and that finally worked.

Also, sometimes mice like to nest in the box for the air cleaner too. Long story short, a couple times I've been troubleshooting cars with very little power and that was the problem.