Remove the saddle by unscrewing it from the sill with a screwdriver or prying it off with a pry bar. Cut stubborn saddles in half with a reciprocating saw then pry each half up with a pry bar. Be careful not to cut into the flooring or door frame when cutting saddles in half.
Check the sill for damage. Leave sills that are undamaged. Cut damaged sills into a middle piece and two side pieces with a reciprocating saw. Remove the center piece by tapping on the underside of the sill with a hammer. Pry the two side pieces off the door jamb with a pry bar. Cut off nails from the door jamb with a reciprocating saw.
Purchase a new sill if needed by using the old sill as a guide. Fit the sill into the bottom of the door jamb. Remove the sill and place tapered wood shims under the sill to angle the sill away from the house. Remove the sill. Squeeze silicone caulk to the bottom of the door jamb and set the sill in place. Tap the sill with a wood block and hammer to secure it in place. Drill pilot holes every 4 inches across the sill. Drive 3 inch galvanized screws into the pilot holes.
Cut wood saddles with a jigsaw so they fit into the door jamb. Create a notch in the bottom of the door jamb stops with a hammer and chisel for metal saddles to fit into the door jamb. Test fit the saddle by setting it over the transition. Adjust the saddle as needed.
Apply a bead of silicone caulk to the back of the saddle. Set the saddle in place. Screw 1-½ inch galvanized screws into the saddle to secure it.