None of the rodent's nest could have made it into the cylinder unless there was a gaping hole in your air filter element. That assumes, of course, that the nest was on the dirty side of the element?
Your compression test is invalid if you did it with bent pushrods.
Did you see any evidence on the top of the piston of the piston hitting the valves?
When did you do your last routine maintenance, including adjusting the valve clearance?