It takes more than a single injection of B12 to correct a deficiency.
Apparently the team immediately knew that Lou had secondary amyloidosis (amyloidosis caused by another condition or infection) as opposed to primary amyloidosis - which is what it's been every other time amyloidosis been mentioned on the show.
At the beginning of the episode, House is shown supposedly playing an Xbox 360 in Coma Guy's room. The control pad is shown to have a blinking green light, which means that the controller is either not connected to an Xbox, or has failed to connect. If House were actually playing the console, the light on the controller would be a single continuous green light.
At the beginning of the episode, Coma Guy's hand repeatedly moves when House takes and replaces his drink cup.
Lou may have been too unstable for general anesthesia, but there's no reason why they couldn't have used IV sedation, local anesthesia, or at least painkillers.
A doctor doesn't start chemotherapy for lymphoma without first determining what type it is.