I think you may be one step ahead of Cherries just by having a plan. I agree with you that this team can't be fixed by nibbling around the edges. It has so many problems that it is hard to figure out what should be addressed first. The starting pitching is the biggest and most obvious problem. It was obvious last off season, and he failed to address it in any meaningful way. If he was relying on there being a treasure trove of FA pitchers this off season, he was brutally mistaken. They all re-signed and extended with their current teams. I had predicted that would happen. Teams don't let young stud starters walk away if they have a profitable fanbase. Now, with only Greinke available, he'll have to get creative, and I have no confidence that he is capable of that.
People are going to criticize you for suggesting trading of Pedroia or Ellsbury. The decisions ahead for Cherries are not going to be easy. He may have to make a move like that to get top pitching in return. I never believe in trading an every day star for pitcher, but the question to be answered is whether Pedroia is truly still a star performer. When healthy and performing, he drives this team without a doubt. His heart is as big as they come, but are his skills slipping. This is what the FO gets paid to figure out. If Pedroia shits the bed next season hitting .250, people will moan about how unexpected it was for him to drop off like that. ********, they get paid to be experts at this stuff. They have all sorts of coaches and scouts. When a guy is starting to decline, they need to know it before the rest of the world. If they think he is still a star performer, keep him. If he is starting to slip, move him while he has value.
As for Ells, I'd keep him for another season to figure out what he is.