Only reason I worry about the animals chewing on the wires is because they have here many times.
-A rabbit chewed threw an extension cord for Chistmas.
-Mole chewed on control valve wire the other day. Luckily it was just the outer jacket.
-My cat chewed on my speaker wire for the stereo system.
-Squirrel chewed fountain cord.
Luckily no animal was hurt in any of the processes.
I would definatly try to get the animals/nest out of the box. Seal the holes with that "Great Stuff" foam, and put a repellent or something in. They'll start messing things up in there, and chewing threw the poly pipe (if you have that)
Edit: I forgot your putting the valves above ground