I moved the faraday for the CCW return path back into the middle of the MM telescope, where the waist is. It turned out that the CW PD interfered with this, so I had to also move this back to the waist of the other MM telescope. The beam wasn't quite at 4" through the telescope so I had to alter the height, which in turn un-aligned the beam for the CW input path.
I was able to get it looking like the input beam and the reflection beam were not clipping on the outside of the faraday. Measuring the power that was being transmitted through the faraday into the cavity there was no measurable loss. However, when I looked at the beam rejected out the side (going to the PD) it was very weak. I found that you could increase this by twisting the faraday slightly, however even then I was only able to get 1.26mW out of 1.56mW that was going in. This is a serious disadvantage to this Faraday design!!! You cannot see where any clipping is happening internally, even when the beam in is small at both sides, and there is no clipping on the outer apeture. It would make life a lot easier if the input and output polarizers were separate.
Next I started aligning the beam back into the cavity again. Of course we haven't touched the cavity mirrors so that is still aligned. The CWW input beam had also become misaligned, though I have no explantion for this. There were a few mirrors with screws that were not very tight, and I tightened them down. Afterwards the CWW input beam was misaligned, so either something moved as I tightened it or I bumped an actuator. After getting the beam vaguely aligned I then looked back at the faraday again. Of course the return beam is now misaligned.... now I can't get more than 50% of the beam back through without clipping.
I think that this is going to require some iteration. We'll need to just keep trying to keep the faraday aligned as we get the beam back into the cavity.