My situation is similar, but nowhere near as severe. I have to question the calcium carbonate rock having much if any effect though? fine ground lime takes long enough to do anything let alone the stone. If anything I'd try to make a rock formation within the pond and over time they should dissolve as needed.
To me I would 2 prong this. I'd lime the runoff source land as well as the actual BOW.
I have a friend that works in the mining and exploration industry. He tells me that when they get set to abandon a mine to become a pond/lake they bring in ton after ton of lime in preparation.
Not an expert, but I'm learning...
