The lenses I'm using for the mode matching telescope are Newport KPX103 AR.18 (175mm) and KPX097 AR.18 (125mm). I contacted to the company to check how the focal length would change for 1064nm. These focal lengths are calculated for a wavelength of 589nm, but the index of refraction for the BK7 glass they're made of decreases from 1.51673 at 589nm to 1.05663 at 1064nm, so the focal lengths increase by 2% (assuming a thin lens).
If I left the lenses in their current positions which were calculated for 125 and 175mm, this gives a power coupling value of eta=.7674, so I have calculated the new distances for the adjusted focal lengths of 127.5mm and 178.5m. The 125mm lens should now be located 597.42mm from the mirror at the corner of the table (4w2l), and the 175mm lens should be 345.21mm from that. These positions give eta=.9910.
I've plotted how eta changes as a function of the lens positions as well. Lens 1 is the 125mm (or rather 127.5mm lens) and Lens 2 is the 175/178.5m. These plots cover +/- 10mm from the calculated ideal position. For lens 1 this value is 597.42mm, as quoted earlier, and for lens 2 it is 2383.46mm, which is the distance from lens 2 to the input mirror.