While I'm not super happy about it I think I found the root of my son's reading/comprehension problems. This might answer a ton of questions and is a step in the right direction.

And the reading program we have been doing at home is really helping. Finally some light in what has been dark for a few years.
High Priestess JessMess, follower of the Goddess of the Coiling Way and Confiscator of Concoctions in the Order of the Curly Crusaders