Wow, I can see why you were proud of it. I hadn't realized it was modular (I thirst do a board like this myself). Have you done any work on it since you discovered the damage?
I know you seriously want to salvage this, but where to start is tricky. You're going to just have to be brutal with it I think. I would suggest, in an effort to avoid illness from the urine, while handling this with a dust mask and latex gloves, serious taking off the top layer with some sort of sanding tool . All that flock and basing materials probably sponged up the nastiness and needs to go. I'd then relayer it heavily perhaps even making the top soil level a few millimeters higher than it was origionally. That way if the foul mouse liquids have seeped in to the core it'll be buried and sealed over. I have no idea how you'll go about saving the river sections, you may have to suck it up and totally redo those sections.
I realize this isn't much advise, but I'm actually attempting to be helpful and it's better than my first post on this matter! Good luck!
