At Northwestern, he completed 507 of 920 passing attempts for 6,822 yards and 42 touchdowns. Kustok also rushed for 1,294 yards and 22 touchdowns on 433 attempts while starting all 23 games in which he played over his final two seasons. He was an honorable mention All-Big Ten choice as a senior in 2001 when he completed 231 of 404 passes for 2,692 yards and 20 touchdowns, with only 10 interceptions. Kustok also was the team's second-leading rusher that year, gaining 580 yards on 175 carries and scoring 11 touchdowns.
Kustok was a two-time team captain and two-time all-league selection, as well as an academic all-state selection, at Carl Sandburg High School in his native Orland Park, Ill.