First, Naked Lunch, to me, seems pretty different in literary writing styles, if that's what you're looking for. Burroughs has this jigsaw story structuring that annoys some people tremendously. I like it, personally. I think Naked Lunch is an amazing book, but if you were to open the book to a random page, quite often you are opening the book to some sort of highly detailed rape scene of sorts. That is how it differs from Clockwork the most. It's a lot harsher.
Do Androids Dream Of Electric Sheep?, the book used for the movie Blade Runner is an awesome read. It is different from the movie in a multitude of ways. The biggest difference being that it has more symbolism and themes going for it than the movie. Philip K. Dick is one of my favorite authors because his books mess with the human condition, instead of expressing opinions, he just changes ideas in his own world. I recommend it. I also recommend Naked Lunch if you're up for it. Another good Dick book is A Scanner Darkly, which just had a movie made after it.
On Clockwork Orange, the reason why the movie left out the last chapter of the book is because it was made in America. Why is this different? The American publisher forced Burgess to keep the last chapter out of the American version of the book when it was originally printed here. It would be a different story now because they added the chapter in current editions of the book, but that's the reason why.
It's hard to watch a movie you've read the book for without expectations, and vice-versa, but they are both different mediums, so they'll be different. Watch a movie like a movie. Read a book like a book. Although movies are much more often criticized for the lack of things that were present in the book.