I feel the movie makes it clear that Elizabeth is the progenitor of the heists target painting, and through her manipulation of Simon, coerced him into approaching Franck with the inside information required to pull off the heist.
Elizabeth hypnotizes Simon to 'Steal Something' for her, something of great value. Knowing that Simon is an art dealer, that he has access to the Goya that is loaded with significance for the couple (and that he is potentially psychotic and has latent violent attributes) she perhaps didn't doubt that he possessed the aptitude to attempt a theft: perhaps the Goya was the most obvious target.
I don't think it necessarily mattered whether she believed Simon would pull of the heist or not, the aim was to place him in some kind of situation that would remove him from her life. If Simon failed, he would be imprisoned or killed. If he succeeded he would be living in the criminal world, or on the run. Any scenario creates distance between him and her.
Remember! Elizabeth doesn't want to take possession of the painting, she only wants Simon out of her life forever.
This is why she is so surprised when he shows up in her office. Her actions have resulted in a very specific scenario, perhaps the only possible scenario, that led Simon directly back to her office. The turn of events isn't about destiny, its about the subconscious: the mind wants what the mind wants.
Outside of universe, the Goya is only sought for its monetary value: the fact it is so meaningful to the former couple is a nice narrative addition, but is ultimately inconsequential other than as another control mechanism for Elizabeth to punish Simon.
Also, she is perhaps the best fit as to who is the movie's true 'mastermind' because she inhabits the role of that old movie trope: the unreliable narrator.
The films climax reveals that she is in possession of almost all the facts from the outset, or certainly more than anyone else.
It is only when Simon's memory returns that she learns more information, which would identify the Goya. She has played Simon through hypnosis, and the rest of the gang through persuasion and feigned ignorance.
The scene's closing moments, when she demonstrates her almost supernatural powers of hypnosis over Franck (by presenting him with the option of being brainwashed to 'forget' all the hurtful memories), compounds the fact that she is in almost total control of the situation throughout.
I didn't see this as being unclear to be honest, but perhaps I've missed some plot holes that draw discrepancies to my interpretation of the plot.
If you are unsatisfied with my answer, could you explain some of the plot holes you mention; either in your question or the comments beneath my answer?