Um, it does sound like you're going through a rough time. But I would stop the CIO immediately, especially if he's crying for hours. Is it really helping you to sleep better? He is probably very confused and needy right now, and one thing that helped us was for me to MULTIPLY my affection and attachment towards my child when she felt that way. As in, when you are home, try to always be holding him, cosleeping, spending lots of time together. Take baths together, walks together, cook together, etc. If you're in school, I know you have homework too - can you do it near him? Can you take next quarter off and just work and spend time with your kid? I did what you're doing as well (FT school, PT work) and the cosleeping really helped us to reconnect.
I like the Playful Parenting guy's description of the "cup" of affection and attachment. If the child's cup gets too low, they let you know it (i.e. crying, acting out, sleeping poorly, etc), which in turn takes more out of you. If you act to fill the cup, you will get a more securely attached child and better behavior in the long term.