since I am syncing the h9k from an SSL alpha link converter via WORD CLOCK and passing the word clock along to an fireface 800 where it is being terminated, i would have to choose word clock in emote, right?

This is correct, Word Clock should be selected in the H9000 if you're syncing from an external device.  You shouldn't need to set the sample rate here, it should be assumed from the word clock stream.  If the clock is locked, the selection will remain stable on Word Clock (if there is no lock, it will revert back to Internal after a second).  The error you're seeing about the USB is a somewhat separate issue relating to your computer's sample rate.  Here is the last part of the section from the manual regarding setting up USB audio:

If you change the sample rate in the DAW first, you will have to change it again once the H9000’s clock is changed to match. This is because the H9000 cannot force the computer to re-sync at the new rate; the computer has to initiate this process.

If your H9000 is successfully locked to Word Clock, you shouldn't need to toggle it back to Internal on the H9000 side, you should only need to make sure that the sample rate of your host computer matches the rate of the Word Clock source.  However if the computer was set before the WC sync was established, you might need to switch to a different rate on your computer, then switch it back again to get the USB error message to go away.