Those increases in numbers is the most likely cause for her being "off" & a bit cranky - the build up of toxins makes one irritable.
Ask your vet about starting her on Azodyl http://www.vetoquinolusa.com/CorePro...al/Azodyl.html
In regards to the phos rising even on a lower phos foods:
Her kidneys can't excrete enough phos so it's building up, even on a food with the lowest possible value the blood phos would still rise because nothing is going out.
The phos binder will not remove much/any of the blood phos but it will prevent absorption of more phos from the food which is why while on a phos binder a kidney cat can safely eat a higher phos food.
Just a guess but the vet likely circled the calcium because the use of calcitrol will cause an increase in calcium values
The ideal Calcium to Phosphorus ratio for cats is 1.2:1 so her numbers fall not too far off 1.16:1.
The changes in calcium levels especially and also phos levels would be determining factors for the dosage amounts, since calcitrol basically regulates the production of calcium.