My study student is so far behind that comprehension is very difficult to get at. He is so used to not knowing how to solve a problem or get an answer that"I don't know" is his answer for everything, even when he does know. I have seen that if you stay away from the worksheet questions and try to create some that are catered specifically to him that there is some, albeit not much, progress shown.
Being so far behind, the books we read together are simple books that are three to four word sentences on a page. These are hard books to test comprehension on, and ask questions so I have tried to quiz him on the books that he listens to. This also provides a challenge because he is so used to throwing the I don't know card, he uses it all the time. I have seemed to be able to get him to talk about the books that he really enjoys, but it is hard to continuously use those books, as they are not of great substance.