For 6 grand, I would pay for the water! 1/2" a day is certainly within the range of normal for some ponds in certain weather conditions.

With the falls off the water level will drop to the lowest current leak, if any. So in theory a hole is pretty easy to find. You can also sometimes see a bump up of dampness at the waterline where the hole is.

Muskrats generally dig pretty high up, like no lower than 1' below the water line. They wouldn't be expected to dig like on the bottom...but they do whatever they feel like doing.

It seems like maybe you're not sure if there is a leak or the loss is from evaporation? A fairly straight sided container almost filled with water and set in the pond on blocks or whatever will show you the evaporation rate. And of course you have to figure in draw down for waterfalls, streams, filters.

It doesn't sound like the new pond would do anything to solve the muskrat issue. Consider mortared rock over liner. That could be done to the current pond once the leak issue is solved.
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