Last week I scanned the SHG temperature for more data points to confirm the dip in the middle of the sinc function. A rough fit to the side lobes suggests we should have about 160mW of green output. A few days before we improved the PMC alignment we measured 230mW of 1064 input into the SHG. 160 mW would be 69.5% conversion efficiency. This number isn't too far off from the conversion efficiency measurement we took when we first installed the SHG 6 years ago. We have known for sometime that we are missing a lot of green power for the amount of 1064 we put in. This plot makes the picture a bit more clear that we have been indeed losing more than half the green power. The cause is unclear. We have been suspecting the gray tracking in the SHG cryatal to be the cause even though we have a low green finess in the SHG. 

The equation I used to create the fit was A*(np.sinc((T-T0)/width))**2 

Where A is the input 1064 power, T0 is 34.9 C, and the 'width' of the sinc function is arbituary set to 2.5.