Great Questions....and for myself, I didn't know the Rennet had a shelf life. I do have it in the fridge and I used the one that came with the kit. I have my own Rennet I'll use next time. Also I added the Rennet to RO Water. Now, I will say, that the water was from water cooler which has both hot and cold water. I did use the hot water side (120+F). Could that be the issue?
I know this is old but I came across the thread and to answer, yes, you denatured the rennet using hot water. I actually put water in the freezer for a bit then the refrigerator, and prep everything so I can dilute, stir, add, and up/down agitate for a minute or so then still as quickly as possible, as the enzyme coagulation starts almost immediately.
Aged rennet can be a factor as well, but the fact you used hot water was the culprit.
Just a note on using pasteurized milk. Pasteurization is bad, but unless it's ultra-pasteurized as mentioned here, homogenization is worse. It's murder on the fat globules and this can induce some off flavors due to an early beginning to lipolysis (fat breakdown products). If you can get creamline from a known farm, even if they pasteurize, you're ahead of the game.
Raw, I'm nuts for it. I drink a ton as I have two brother friends who raise a very small herd of Ayrshires on managed, rotational pastures. Ayrshire is kind of interesting because the fat globules are so small, the milk comes out virtually homogenized already. Also interesting, and I'm not remembering this well, but I believe not only is the breed low on beta carotene, but it lacks the enzyme - CoA? can't recall - to convert the carotene so it pigments the milk yellow during high forage (e.g., summer flush) seasons. A very white milk year around, and a fantastic tasting milk.
I'm with Bernard. I see no relationship between silage and calcium deficiency. It's just inviting contamination. I don't know of any issue of Ca++ deficiency and raw milk.