No he couldn't gather the ball as he had to use his other arm to fend off Davis. He wasn't trying to do this: <iframe width="420" height="315" src="https://www.youtube.com/embed/s5bqF4VDSx4" frameborder="0" allowfullscreen></iframe>
I though the ref's have some control over starting the clock (maybe this has changed again) because of the Utah incident. Watching the play again, the clocked was stopped because the play should have been blown dead at .3, so they anticipated correctly but the ref on the base line keep letting the play go on. Then, they realized, "he didn't stop the play!", start the clock again...