Prepare the shortbread crust as directed.
In a heavy 2- to 3-quart saucepan fitted with a candy thermometer, combine the brown sugar, honey, salt, and water. Set on medium heat and add in the butter. Stir constantly with a heatproof spatula, scraping the corners and bottom of the pan as the butter melts. From time to time, scrape the mixture off the spatula against the top edge of the pan and scrape the sides of the pan clean.
Bring the mixture to a medium boil and continue stirring and scraping the pan for about 3 minutes, dissolving the sugar.
Stir in the condensed milk and return the mixture to a boil, stirring constantly, scraping the sides, corners, and bottom of the pan to ensure that your caramel doesn't burn. Adjust the heat so the mixture boils actively but not too furiously. Continue stirring and cooking until the mixture registers 235°F on a candy thermometer. Total cooking time will be close to 15 minutes.
Remove the pan from the heat and stir in the vanilla. Scrape the hot caramel over the warm crust.
Tilt the pan to level the caramel. Scatter the toasted pecans and chopped chocolate over the surface and set aside until the caramel is cool and the chocolate is set. (I let the caramel set slightly, and then spread melted chocolate over the caramel, and sprinkled the pecans on top. Feel free to use either method, both work wonderfully!)
Slice the bars into relatively small pieces, they're very sweet. I've found their easier to slice when chilled. Keep in an airtight container for up to a week. Enjoy!