Honestly you are asking a lot. Adding some muscle in strategic places in 6 weeks in possible... losing fat in 6 weeks is possible. But adding muscle in strategic places while losing fat (so assuming a caloric deficit) only lifting twice a week is very very optimistic to say the least. I'm not saying you wont see any improvements but it wont be that significative, at least in the muscle mass department.
I also don't like of not doing any work for other body parts for 6 weeks. Sure you could argue that the main lifts used will work all muscle groups to some extent. And that might be true. But there is a difference between "involving" a muscle and stimulating enough so that it grows or at least maintain its size.
First I would not worry about the lifting sessions interfering with the conditioning work. First because growth factor training doesn't lead to a lot of soreness and also it doesn't burn out the nervous system. And even if it did, so what? It's not like you will be tested on your performance in a GPP workout.
As for the amount of sets for growth factor work, you can realistically do 2-3 complexes (on one day do 3 for one body part and 2 for the other one, and reverse the order for the other session) for 3 or 4 sets each.