Edit: More reading on Wikipedia has thrown up this sentence that is so important I'm putting it at the top. Again, it supports my first impression of using agile and EV:
Because EVM requires quantification of a project plan, it is often perceived to be inapplicable to discovery-driven or Agile software development projects
Original post follows:
One of the fundamentals of agile is that you don't define the whole project at the start; you define and clarify it as you go along, which means the requirements are more up-to-date when they're needed and the project owner has the flexibility to change what is most beneficial to the project. Defining all the requirements up-front in such detail you can count every single story is exactly what agile tries to get us away from.
I've not calculated EV with agile before (because in and of itself it seems a little difficult to combine the two), but having a quick read on Wikipedia, it highlights what I thought:
Agile embraces change and therefore scope is considered variable (i.e. not fixed). Instead of using the INITIAL estimate in total number of Story Points, in Agile EVM calculations always the LATEST estimate in total number of Story Points is used to calculate CPI, SPI, EAC, etc.
So, as @aqwert mentioned above, you will most likely need to start listing your epics and themes, breaking them down as much as possible to get an estimate of stories which you can then start using to calculate. This still feels wrong to me: defining as many items as you can up-front in agile. My gut feeling is that whoever wanted to use agile but also want up-to-date EV from the beginning of the project doesn't understand one of those two (in the nicest possible way).
The last thing I'd say is that you won't know how much EV goes towards a story or story-point until you've been on the project for long enough to learn this. Each team has different velocities and effort for each story point, so you will need to update as you go and as you learn. Once you have a good understanding of velocity and correlation between stories and EV, the more accurate your future calculations will be in the future.
Good luck and thanks for all your input on this SE network; you insight has helped me a lot over the years.