dx/dt = k * C * Y / (K + Y)
where C = [calcium/calmodulin]/[total calmodulin]
You would declare A as a modifier
dx/dt = k * P * Y / (K + Y)
where P = pH
You would not declare P as a modifier, but as a parameter
Even if pH is in fact proportional to the concentration of H+"
In the case of the reaction controlled by calcium:CaM, yes I would definitely expect calcium:CaM to be a species and to appear in the ListOfModifiers.
In the case of the pH-controlled reaction, if H+ is in the ListOfSpecies, but not in the lists of Reactants or Products for the reaction whose kinetic law you have written, then I WOULD declare H+ as a Modifier even if P were defined by
P = -log[H+]
If P is constant, then yes it could be a parameter, but I imagine most people would lump it into the rate coefficient, k.
In the case of the assignment rule:
"Consider the following assignmentRule:
parameter X (not an entity pool)
if CONDITION 1
then Y = A
else Y = X
What is Y? "
I don't think Y can be identified as a reactant, a product or a modifier.