Thiago is out due to injury.
Costa and Negredo would be the more logical options for strikers, it's unlikely Krusty will be fielding more than a single striker so two should be enough. I really don't think Villa or Llorente will make it, although Llorente did really well with his post-play in South Africa it's been four years since that and he's not as good as back then.
Mata... I don't really like Mata. I'm still amazed such sums of money have been paid for him in the EPL. Not saying he's not a really good player, but I simply don't have him in high regards.
My guess is for Krusty to stick to his usual 4-5-1, likely with Casillas as keeper and Azpilicueta - Piqué - Ramos - Alba in the back four. I don't know what's he going to do in the mid, Busquets - Alonso - Xavi would be the slowest midfield ever, Alonso has proven this season how much he struggles nowadays when playing more than a single match per week, so I'd use him sparcely and same for Xavi. I guess Pedro will get a spot as his energy is much needed and he always performs fine for the NT anyway. Krusty will need to use his bench proficiently if he wants to last long in the competition IMO. I'd probably stick to Silva as the pivotal player of the team but Krusty's never been a big fan of his.
BTW if Spain doesn't win it'll likely be due to Arbeloa's abscence.