Despite multiple tests they have yet to show any correlation between milk and stone formation.
I'm unfamiliar with MuscleMilk, and moreso with the precise reason for your stones (hypercalciurea means you have too much calcium in your urine, but there are several causes).
For me, stones can form and grow to about 3-4mm in about a month, so your growth is similar in your time span.
The question is, where is your high calcium coming from? The most common reasons are:
Excessively high dietary calcium
And less commonly, rickets. Also, exceptionally long bedrest can cause hypercalcemia or HCU as the bones soften. This is unlikely in your case, clearly.
The real answer here is you have to *have to* go talk to your doctor. It could be that you happened to be skirting the limit of calcium levels and the increase pushed you over the edge. Or that the increase in protein adds just enough extra stress on your kidneys to knock you over a threshold. In either case a simple dietary change will fix it.
But, it could also be that you're flirting with complete renal failure (which can cause hyper-parathyroidism) in which case extreme dietary change, hormone therapy, and more are required so your entire body doesn't shut down.
So... doctor. See one. If they don't give you clear answers, get another. I've been through a bunch of nephrologists and urologists to stick with ones who will explain things, and keep up on the literature. It's worth it. Kidneys are not something to mess with. See a doc.