I manually updated my nexus 6 last night to LMY48I (did the old @bkdodger dirty flash) and today I just got my stuff from Google for Project Fi. According to the rep 48I should be ok for those running Project Fi but i'll find out soon enough.
Did you update to the stagefright patch either via ota or manually yet?
I use Wug's Root Tool Kit and updated the stock image with the latest patch, Wug's has the latest stock image for your Nexus device in his tool kit, just plug your phone into your PC open the tool kit and new image in a few minutes without wipe.