SAN FRANCISCO — The San Francisco 49ers signed free agent linebacker and special teams standout Dan Skuta to a two-year contact Thursday. The team made the announcement late Thursday, on Day 3 of the NFL’s free agency period. Skuta, 26, spent his first four seasons with the Cincinnati Bengals. Skuta made 26 tackles last season and a team-leading 17 tackles on special teams for the Bengals. He now joins one of the best linebacking groups in the NFL — featuring Patrick Willis, NaVorro Bowman, Aldon Smith and Larry Grant. So, breaking into that defense might be a tough task on …