Did you check the intake plumbing downstream of the filter for dirt contamination? Unless I'm looking at the picture wrong, it appears that your friendly mice created a decent amount of area through which air might pass unfiltered to the engine.
I very well know that mice do this (shack up in airboxes and other inconvenient places), but I'm baffled as to why. It may seem to be a nice cozy home when they find it, but I'd think that after the first startup after move in, they'd learn to go elsewhere. I can't imagine that they'd enjoy the noise and windblast that would be constant in the airbox while the car is running???