The free agents enabled the 49ers to jump from the 18th-ranked defense in the league to the 8th, and to jump from the leagues 16th-best defense against the run to the 2nd. Pro Bowl defensive lineman Dana Stubblefield led the team with 8.5 sacks. Rookie defensive tackle Bryant Young was also a big threat to opposing quarterbacks and rushers, recording 42 tackles, 6 sacks, and a fumble recovery. Behind them, Norton played very effectively at the middle linebacker position, leading the team with 77 tackles and recording an interception. Pro Bowl safety Merton Hanks led the team with 7 interceptions for 93 return yards, while Sanders had 6 interceptions for 303 return yards and 3 touchdowns, earning him the NFL Defensive Player of the Year Award. His 303 return yards was the third-highest total in NFL history, while his touchdown returns of 74, 93, and 90 yards made him the first player ever to have two 90-yard interception returns in one season. Pro Bowl safety Tim McDonald was also a big contributor, recording 2 interceptions for 79 yards and a touchdown.

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Which player had more touchdowns in the Pro Bowl, Tim McDonald or Sanders?