Overall transmission: 95%
About 95% of the power going in is S-pol so the transmission was calculated based on everything that came out over S-pol power that went in. The half wave plate at the output of the isolator hasn't been fixed so it still spits out mostly P-pol. About .5% of what came out was S-pol (a half wave plate has been installed to fix the polarization).
Isolation: -30.5 dB
Usual set up: Mirror facing flat at the output and beam splitter at the input. I found a non-polarize beam splitter for 1064 this time. Assuming no losses in the reflection I measured the power that came back through the isolator and reflected off the beam splitter. Taken the known input power and the percentage of the reflected power before going into the isolator into account I calculated the total power that came back through the faraday.