Hello mike...
I doubt the rocks from a freshwater lake could do such a job on the tank chemistry in all that water in just 3 days. Did you fill the tank to the top with rocks? Retest the pH for starters and drop some vinegar on one of the rocks. If there's a reaction, don't use it. The water change was a good move. Half the tank water should be change weekly anyway, no matter how large the tank.
A nitrate level of 40 ppm isn't a reason for concern. Most aquarium fish are fine with a higher nitrate level for a short time. At worst, they'll feel a slight discomfort. Get some floating plants like Hornwort into the water. They'll help use the nitrates.
Start a more aggressive water change routine for a few weeks and see how the fish do. I doubt you've done any damage.
B