Preheat oven to 350°. Put pecans on a rimmed baking sheet and cook, stirring occasionally, until toasted, about 8 minutes. When cool enough to handle, chop roughly. Divide into 2 batches; chop 1 batch finely. Set both batches aside.
Put sugar, butter, salt, and 3/4 cup water in a 4-qt. saucepan over medium heat (see Notes). When butter and sugar are melted, increase heat to medium-high and cook, stirring occasionally, until mixture is deep golden brown and measures 310° on a candy thermometer, about 20 minutes. Remove from heat and carefully stir in vanilla (mixture will bubble up) and finely chopped pecans. Pour into a 10- by 15-in. rimmed baking sheet. Let toffee cool until set, at least 30 minutes. (For even pieces, you can score the toffee by cutting it with a sharp knife after it has set for about 10 minutes, scoring into 5 strips lengthwise and 8 strips crosswise to yield 40 pieces. Wipe knife clean with warm water after each slice for easier cutting.)
Chop chocolate and put in a medium metal bowl. Fill an 8- or 10-in. frying pan with 1/2 in. of water and bring to a boil. Take off heat and put bowl of chocolate in the water. Let sit about 5 minutes. Stir chocolate until melted. Pour over toffee; with a knife or offset spatula, spread evenly. Sprinkle chocolate with roughly chopped pecans. Let sit 20 minutes, or until chocolate is cool but still a bit soft. Sprinkle with sea salt. Chill until set, about 1 hour.
To remove, gently twist pan to release toffee, then chop or break into chunks. Store in an airtight container.
Use caution when working with sugar syrup, as it can cause severe burns. Set out your baking sheet so it’s ready to use, and keep ice water nearby to cool any burns. Toffee keeps at room temperature in an airtight container up to 2 weeks; chilled, up to 1 month.