I've replaced the SM fiber in the 1064 nm launch with a PM fiber (P3-1064PM-FC-5). I also moved the fiber collimator (F240APC-1064) back 2.54 cm back to give more space for a PBS cube (to check linearly of the light).
For the 1064 nm launch it seemed to be a lot harder to find the initial alignment of the collimator using the alignment of the back propagated 650 nm fiber laser source. Here I aligned a pair of irises in the forward propagating direction and then back propagated through the PM fiber using 650 nm to get the initial pointing of collimator. I don't know why this is so much harder than the 532 nm case. I suspect one of the steering mirrors is not really reflecting off the front dielectric surface. In the end I did a bunch of systematic walking of the fiber launch mount and eventually fount the alignment.
From 4.44 mW of input light I get 2.74 mW of light out the other end of the fiber. This is an efficiency of 62 % which is more than enough for my needs. I expect the HD will only need 1 mW (2 mW max), so this is fine. Getting this in coupling higher will require a bit of lens walking, not really worth it at this stage.
I had already carefully aligned the collimator orientation to put the fast axis on aligned to p-pol (wrt the table), by eye. It seems like the launch pretty much hit the correct launch polarization on the first go. I see little variation in the polarization when I pulse the heat on the fiber. This is now good to go for optimizing the homodyne visible and polarization overlap output from the SQZ.