Stevenson's "Treasure Island" has a couple of main conflicts that arise throughout the novel. There are other small conflicts scattered throughout, but naming all of them as your question implies is extremely difficult. There is guaranteed to be something that I don't consider a conflict that another reader may consider a conflict. I'll attempt to point out the major conflicts of "Treasure Island."
At its core, "Treasure Island" is a coming of age story for young Jim Hawkins. He starts off as an obedient, quiet boy who is easily frightened. As the novel progresses though, the reader witnesses Jim's transformation. Throughout the story, the reader sees Jim grow into a braver young man. He begins to take more initiative, and his quick, agile mind proves to give him a cleverness that was not introduced in the beginning of the story. The conflict here is Jim's battle with himself. It's the classic "man vs. self" motif. Each event in the story forces Jim to dig deep within himself and overcome his previous fears and hesitations.
If Jim himself is man vs. self, then the man vs. man conflict in the story is between Jim and Long John Silver. Silver is Jims's main antagonist. I could really choose any of Silver's pirate band to be an antagonist to Jim, but I choose Silver, because he is the leader of that group, and Jim has the most contact time and interaction with Silver. The reason Jim's conflict with Silver is so large and important to the story is because Silver himself is an extremely complex character. He quickly switches back and forth between murdering brute and charismatic leader and friend. Jim even publicly proclaims that Silver is "the best man here." With that said though, they are not friends. Silver may like Jim, but he doesn't hesitate to threaten and use Jim as a necessary means to an end.
Another main conflict is a group conflict. It is the conflict of Silver and his pirates vs. Smollett and the remainder of his loyal crew. There are a couple of battles between these two groups, which make for exciting reading.
The last main conflict, in my opinion, is the conflict between Silver and his own men. It's has to be tough to be a pirate leader, because pirates aren't known for their loyalty in the first place. Silver and his group are no different. Silver is constantly struggling to maintain control and order over his men. Sometimes it's through violence and threats. Sometimes it's through bribery and word trickery. No matter what though, the reader gets a sense that Silver might lose control of his own men at just about any moment.
The Protagonist of the story is young Jim Hawkins. He comes across as a sincere, adventurous sort. He is brave and can get out of tough situations due to his mental agility. His first person account of the happenings endears him to the readers.
Jim Hawkins’ antagonists are his childhood anxieties and his unpredictable behavior. He has many other antagonists in his life like: Black Dog, Old Man Pew, Long John Silver, Israel Hands, etc..
The climax of the story occurs when Jim Hawkins accidentally walks into the enemy camp and gets captured. It is for the first time, after the war was waged between Captain Smollet and Long John Silver, that a man from the opposite camp is captured. Jim’s capture also results in the downfall of Silver when his men lose their trust in him. It is with Long John Silver that Jim travels for the remainder of the adventure.
The outcome of the story is the victory of good over evil. Saving the treasure from the hands of the pirates by the good men of law and their safe return also records Jim’s journey from an immature boy to a responsible young man.