For the second-straight week the Dukes (2-0) had more than 600 yards of offense.
Lee completed a 13-yard pass to Cardon Johnson for a 7-0 lead.
Johnson got his second score on a 3-yard dive to make it 17-7. Brandon Ravenel forced a fumble that Rashad Robinson recovered and returned 34 yards for a score. Khalid Abdullah scored from 5 yards, and Lee scored on a 17-yard run to make the score 38-7.
Shafnisky threw for 263 yards and ran for 53 for the Mountain Hawks.
Lightning delayed the game 30 minutes in the fourth.
AP College Football website: www.collegefootball.ap.org