Add two return ducts, one in the guest room and one in your sons room. This will give the system the air it needs to breath properly and increase the comfort in those rooms New drainline down the side of the house. This will remove the upstairs drainline from the main floor systems pump. this will increase the life span on the main floor pump and decrease the chance of flooding the basement. New properly sized supply plenum. This will drastically fix the airflow upstairs and make the system be sealed properly.