Fixing your diet will be key to your recovery and muscular gains.
As for the training, you may be doing a little too much and not able to recover fast enough.
I would recommend using a template similar to Westside for Skinny Bastards:
One idea would be to have a max-effort day where you focus on a pressing movement for low reps and high weight followed by some assistance lifts for the bench, back, shoulders and arms.
The next day could be a dynamic day where you work on some explosive lifting using plyometrics like med ball throws against a wall or to a partner or some light but explosive benches along with some assistance lifts for arms and shoulders.
The third day could be a repetition-based day where you can use more bodyweight exercises and work your chest, shoulders, back, triceps and biceps.
You may want to ask Joe Defranco this question on the Elite FTS site (www.elitefts.com). He’s good about responding to questions within 2-3 days, and I’m sure he could give you some good ideas on how to structure your training.