Wrap a double thickness of foil around a greased 9-inch springform pan.
Combine flour, brown sugar, and pecans; cut in butter till crumbly. Press into bottom of pan. Place pan on baking sheet, bake at 325 degrees for 12-15 minutes or till set. Cool on wire rack.
Beat cream cheese and sugars till smooth. Beat in 1/4 cup flour, cream and vanilla. Add eggs, beat on low speed just till combined. Remove 1 cup batter to a small bowl; stir in melted chocolate until blended. Spread over crust.
Combine caramel topping and remaining flour; stir in pecans. Drop by tablespoonfuls over chocolate batter. Top with remaining batter. Place springform pan in large baking pan, add 1 inch of hot water to larger pan.
Bake at 325 degrees for 1 1/4 to 1 1/2 hours or until center is just set and top appears dull. Remove pan from waterbath. Cool on wire rack for 10 minutes. Carefully run a knife around edge of pan to loosen; cool 1 hour longer. Refrigerate overnight.
For ganache, place chips in a small bowl. In a small pan, bring cream just to a boil. Pour over chips; whisk until smooth. Cool slightly, stirring constantly. Spread over cheesecake. Sprinkle with chopped pecans. Refrigerate until set. Garnish with pecan halves and additional caramel topping if desired.