Problem 1
"I'm on my way, but now I'm worried that while I'm trying to be healthy (and watch my sodium because I have a history of kidney stones), drink enough water, eat lean meats, plenty of veggies and fruits, healthy oils, etc., "
It is real easy to increase calories by eating fattier cuts of meat. Real easy and real tasty.
Problem 2
"I know it's not about the numbers on the scale, but I'd like to see those numbers start to decrease! "
The number on the scale is only half the equation. Get a cheap pair of calipers and find your estimated BF. Then you can watch for a downward trend in BF no matter what the scale says. You may see the numbers decrease but you won't know if it is fat or if you just had a great bowel movement.
Problem 3
"And I'm trying to keep my carbs under 150g/day and while I've been doing good at this, I'm only eating around 1200-1300 calories a day"
Decrease carbs to less than 100g. By increasing the fat in your meats you will increase you energy available and avoid the shakes.
Problem 4
Crossfit + severe calorie restriction (1200 in this case) = cortisol = forget about losing fat. Either rest more, eat more, or Crossfit less.
I always assume people know what I am talking about. Big mistake.
Not that I think you should know what I am talking about. Bah! See what I mean haha!