Hard PVC pipe going from the flexible copper will not stand up to the flex that can be applied to the fittings/pipe. That is why copper and then PEX was used. Based on your description of the events I would assume that the PVC is the culprit too. There are flex copper lines with threaded fittings available that have a sufficient diameter to allow flow available at HD and Lowes.
I would not worry the black tank being the source of the leak. There may be some seepage from the flange where the toilet sits on the floor, but I would get it dry before digging too deep. I had a WH burst on me and the water went everywhere.
If a faucet had been running and pumped the entire fresh water tank into the grey holding tank, the shower/tub would have been filled with water too from the backup from the gray tank.
On replacing the hook up for the WH I would say if you can DIY you are looking at less than $50.00 and three trips to the store.
All plumbing takes three trips
One to get what you think you need, one to take 60% of what you bought back and get the other stuff that will fit, and the last one to return all the stuff that you bought that did not fit at all and to buy the one last piece to make it work