Apologies if some of my terminology is wrong (I am merely a PAX!) However, it strikes me that this incident can be divided into two halves, before and after the return of the CPT.
First half, pitot tubes freeze giving unreliable air speed indications and AP disengages. PF continues to fly the plane for a short while but stalls. Pulls the nose up instead of pitching down. This could possibly have been prevented had he have know the attitude and ground speed prior to the failue of the Pitot tubes or followed some standard settings as per a previous post.
Second half, CPT returns from his rest. Perhaps he had been in deep sleep and therefore not fully on the ball. He's met with a dark cockpit the plane oscillating and a whole load of alarms sounding. Firstly, he must have said someting (even WTF) yet there is no mention of this in the transcript.
Question 1: Does he know the plane is in a stall or in a drive? You would have expected that the first things he would have checked are the airspeed, the altitude (dropping rapidly and appears to be displayed as shortlay afterwards the PF states that "we’re going to arrive at level one hundred") and the attitude (presumably still being displayed).
At 2 h 12 min 02 both pilots were reporting no (valid) indications. Question 2: What does 'no' mean. Are they referring just to air speed? This strikes me as unlikely. Could the FDR say that the instruments were showing certain readings whereas in reality some instruments were out?
However 40 seconds after the CPT arrives, the PF pushes forward on the stick, presumably in an attempt to dive and fly out of the stall (exactly the right thing to do). We know that the airspeed increased causing the stall alarm to resound. Question 3: What happens next? Does the PF pull back on the stick to get rid of the alarm (wrong thing to do)? Question 4: At 2 h 12 min 02 the thrust levers were are idle. Were they put there to reduce stresses on the plane in the dive / pull up recovery manoeuvre? Was this the right thing to do?
At At 2 h 13 min 32 there are further inouts by each pilot. Question 5: What were theses inputs (push down or pull up)? Did they continue to attempt to recover from the stall or were they just sat there dumfounded with the nose pointing up?