I've been racking my brain trying to come up with a way to solve this particular problem.
Mind you, I've been reading the properties template over and over again, but I can't seem to find a solution.
The idea is to use a single item model that replaces the emerald item with a rupee.
Then to have that rupee change color by renaming it or possibly altering the stack size.
The base model itself uses 3 different texture files, respectively named rupee_green_(1), rupee_green_(2) and rupee_green_(3).
These images are in their own directory: assets>minecraft>textures>items>custom.
The replacement textures are located in assets>minecraft>mcpatcher>cit>rupees (ex.: "rupee_blue_(1).png").
it doesn't work with models yet. You can only change items whose
"models" are generated from their textures. If your items use a custom
block model, you can't change their models or textures. Not yet at
least. I saw someone suggest it on Optifine's github, and it got marked
as "todo" so maybe the feature might be available in the future.
But for now you can only change textures of generated items.
That's too bad, I guess. At least there's an answer for other people that were looking for the same thing.
I suppose I'll allocate these different models to other items that are not emeralds.