Maybe the citric acid required is different for raw milk vs pasteurized. As I only use raw, I can't really say.
What a horrible waste, though! I really don't like the citric acid method because it just isn't very flavorful, but it will melt on pizza in a pinch.
I dont' particularly like using the microwave for heating my curd, either. I use a basket suspended in a gallon of hot whey with a cup of kosher salt added to it. I cut my curd into 1 inch cubes and allow them to warm up a couple of minutes, then take them out to knead them. I wear a pair of rubber gloves to work the curd and have the whey at about 165-170 degrees. It still gets hot, but I prefer to use my hands.
As I make my cultured mozz in 5 gallon batches, it will take me about an hour to get it all stretched. I make it up into baseball sizes, putting the balls into the whey one more time after I have the ball formed. After a minute or two, I put it in cold water for 3-4 minutes to set it up, then remove to a dry plastic container.