Here are the things we found most useful.
The first few chapters of the book Reading Reflex, by Carmen McGuinness, is extremely informative about the process of reading instruction. There are some assessments in the book that can help pinpoint what issues are present. I didn't use the book for actual instruction, because I think ABeCeDarian is better. It's the same approach, but much more user-friendly.
We did tons of fluency work, but unfortunately my son is still a very slow reader. I think it helped him, but he is maxed out and at his limit. The Six Minute Solution is excellent for fluency, but very expensive.
For comprehension, I like Reading Detective.
There are many other programs and approaches. You might want to post on the Special Needs board. Lots of very experienced homeschool reading teachers over there.