Because the beam profile was normal, I put back the QWP and the HWP and verified if it was s-polarized yesterday. Today, I put the new Faraday Isolator and adjusted it. I measured the intensity without the FI at around 30mW and with at around 27mW. That gives a transmission about 90% and the manufacturer gives 91% of transmission. But because I had trouble adjusting it, I'll do a beam profile tomorrow to check the new FI and the setup.