Hello Roy44! Glad you enjoyed the lesson. Yes, there are many early Cash tunes that are played in the key of F with the capo on the 1st fret. The decision was made to teach the song in E in case students didn't have access to a capo. However, it is very easy to transpose the song by putting the capo on the 1st fret and adjusting all fingerings up one fret.
As you pointed out, the first lick of the solo can also be played at the 9th position using the B and E strings. That is one of the wonderful things about the guitar -- there are multiple spots to play the same thing. I encourage all students, once they've learned a lick in one spot, to find other spots around the neck to play the same thing. This broadens the knowledge of the neck, which is very worthwhile.
The boom-chick-a-boom rhythm can be very challenging at first. Be sure to practice this very slowly before attempting to play along with the track up to tempo. The more time spent practicing this rhythm at a very slow tempo, the more locked into your muscle memory the rhythm will be, and over time, you'll find it easier and easier to play along up to speed with the track.
Cheers!
Mike
Keep rockin!
Mike Olekshy
GT Guitar Coach