Preheat oven to 350°F / 177°C.
Spread pecans out on a sheet pan and toast in the oven until fragrant, 5 to 7 minutes, shaking the pan halfway through cooking. Set aside.
Line a rimmed sheet pan with parchment paper (this will prevent the toffee from sticking). Spray the parchment lightly with nonstick cooking spray.
Arrange saltine crackers in a single layer on the sheet pan. (It’s okay to use broken crackers.)
In a heavy-bottomed saucepan, combine sugar, butter, and light corn syrup. Cook over low until sugar is melted. Increase heat to medium and cook, stirring continuously, for about 5 minutes until the syrup simmers. Simmer for 5 to 6 more minutes until it turns a light caramel color (a candy thermometer should register 300 degrees).
Working slowly (be very careful - the toffee is super hot!) pour the toffee over the saltines. Use a spatula to spread it out to evenly cover the top.
Let the toffee sit for 2-3 minutes until it is cooled slightly and then scatter chocolate chips over top. Let stand until chocolate is melted and then use a spatula to spread the chocolate evenly over the toffee.
Scatter the toffee baking bits and pecans over the melted chocolate. Freeze until set, about 20 minutes.
Melt the milk chocolate in the microwave, stirring frequently. Drizzle in thin lines over all of the toffee. Sprinkle a small amount of flaked sea salt on top.
Return to the freezer until fully set, about 20 minutes more. Carefully invert the toffee onto a large cutting board or counter and peel off parchment paper. Break into pieces.
Store toffee in an airtight container in the refrigerator for up to 10 days. Serve chilled.