Walter does not need to build a Faraday cage in order for the agents to enter the the house from where the time anomaly originates. A car forms a Faraday cage / shield so one could have been driven up the steps towards the house.
When Peter moves back into Walter's on campus house, after Olivia leaves, he picks up the DC 3 toy airplane from the chair. That toy was purchased by his mother for him after he was brought back from the parallel universe and thus would not have been in the current timeline where he drowned in Reiden Lake.