When he first started second grade, he had a reading level of a kindergartener. By the end of the year, he had a reading level of a first grader going into second grade, which was a big accomplishment. But I still am puzzled about his reading comprehension. I would very much appreciate your comments about this. It sounds like the reading problems did begin to show up as your son began to read more.
Comprehension comes later.
However, if he was still reading at a beginning level at the time, the connection to reading comprehension may not have been made. This may have happened later. Most studies don't support the practice of retention, especially for children with learning disabilities. He just needs more time and practice. Unless he's upset by spending another year in the same grade, then retention may help give him the skills he needs to be successful in the coming years.