Vilas,
What I have found works fairly consistently in the low altitude clean stall recovery (and I emphasize this is technique), is after the initial pitch down to wait until the speed trend is trending up and then bring in thrust to about 50% N1 (PW1100). Once the speed is out of Vls, begin gently pitching up at about 2 degrees per second while slowly feeding in thrust with the intent to eventually reach about 10 degrees up and CLB detent.
For the slat extension, sometimes people do that too early and it causes pitch instability. I have seen people call for flaps 1 while still in the initial pitch down, only to have that pop the nose up again and start a PIO. Best to get the nose down first, then call for the flaps.
If the bird is on, one technique one of our instructors uses that I like is to watch the relationship between the bird and the nose. If that distance starts to increase you are nearly guaranteed a secondary stall warning. It helps to learn the proper coordination of pitch and power.
For flap retraction, sometimes this needs to be done fairly quickly as the speed builds up. Over speeds usually happen when someone gets the power in too quickly, and the pitch back up too slow.
The secondary stall warning itself is not considered negatively for grading the maneuver, as long as the pilot makes the corrections.