Your pH is SO low I'm amazed the vinyl liner hasn't dissolved. You FIRST need to get pH normal--add box after box of Borax until you have a ph of at least 7.0 Now you can take your other measures and you may find that CYA is quite different.

You'll have to check the liner for damage from that low pH. I absolutely agree with Waste's assessment of what happened, except for the heater.

Fix pH first, then re-measure the other items.