What is the main conflict in Unwind by Neal Shusterman?

I suppose that different readers might choose slightly different "main" conflicts in the story. I'll highlight a few of the major conflicts that are present in Unwind.  
For me, the most central conflict in the story is a person/people vs. society conflict. Shusterman has created a world in which retroactive abortion is acceptable. The population has bought into the idea that a child's life doesn't end if his/her body parts are farmed out and donated to other people. This process of harvesting teenage body parts is called "unwinding."  

However, between the ages of thirteen and eighteen, a parent may choose to retroactively "abort" a child . . .
. . . on the condition that the child's life doesn't "technically" end.
The process by which a child is both terminated and yet kept alive is called "unwinding."

Connor, Risa, and many other characters in the book have all been labelled for unwinding, and they don't want that to happen. They know that unwinding is a lie, and they know that they will most certainly not be alive after being unwound. These children that aren't willing to go silently to their deaths try to run away. They are then equivalent to escaped convicts, and they are hunted down by a special branch of law enforcement. This is a central conflict. The kids don't want to be unwound, but the government says that they must be unwound. The kids think they will die, and the society thinks that the kids will live on in pieces. 

"I was never going to amount to much anyway, but now, statistically speaking, there's a better chance that some part of me will go on to greatness somewhere in the world. I'd rather be partly great than entirely useless."

Another central conflict to the story is a person vs. person conflict. This particular conflict type is best illustrated through Connor and Roland. The two characters hate each other, and they are frequently physically violent or very near to it. Once at the Graveyard, their conflict escalates as groups of kids begin supporting either Connor or Roland. 
Finally, the book has a major person vs. self conflict. This conflict type is best seen in Lev. Lev is a tithe.  

Lev was a tithe from the moment he was born. You don't undo thirteen years of brainwashing in two days.

Being a tithe means that Lev's parents always knew that they were going to have Lev unwound. Lev is their 10th child, and they feel that they should donate 1/10 of their children to the world. This means that even before Lev was born, his parents planned to give him up to have his body parts harvested and donated to many other people. 

Lev reluctantly nods, knowing it's true. He was a "true tithe." With five natural siblings, plus one adopted, and three that arrived "by stork," Lev was exactly one-tenth. His parents had always told him that made him all the more special.

The internal, person vs self conflict is that Lev begins to question why he should be the one who has to die.  

"Well . . . I've just been feeling jealous of my brothers and sisters. I keep thinking of how the baseball team is going to miss me. I know it's an honor and a blessing to be a tithe, but I can't stop wondering why it has to be me."

Lev has been raised to believe that being a tithe makes him special and unique; however, as events in the story unfold, Lev begins to doubt everything that he formerly believed about unwinding. By the end of the novel, his attitude has been completely turned around. He's still willing to die, but he's only willing to die in the fight against unwinding. Much of the book focuses on Lev being conflicted and struggling to reconcile his childhood beliefs with what he sees unwinding is really doing to young people.