I'll finish up the beat / frequency noise parts of the diagnosis tomorrow later, but I've done some investigation of the AUX X laser RIN. 

I placed a PDA255 at one of the rejected beams from the PBS on the downstream side of the IR faraday, making sure the power didn't saturate the PD. I measured the RIN on a SR785, and simultaneously looked at the signal on a 100MHz scope. 

The RIN has a very strong dependence on the laser diode current, and no noticable dependence on the crystal temperature or the presence of the PDH modulation / temperature control cables. Here are some traces, note that "nominal" current up until recently was 2.0A. 

When adjusting the diode current, a peak beings to appear in the tens of kHz, eventually noticible in the DC power trace on the scope. The point at which this occurs is not fixed.

At all times, I saw a strong intensity fluctuation at around 380-400kHz on the scope whose amplitude fluctuated a fair amount (at least 75mVrms over Vdc=6.5V, but would often be 2 or 3 times that).

I didn't look at the frequency noise while doing this, because the WiFi at the X end was too slow, I'll do more tomorrow in the daytime.