Make the Chile Paste: Combine the peppercorns and annatto seeds in a spice grinder (or use a mortar and pestle) and grind coarsely. Set aside.
In a small saucepan, combine the shallots and oil over medium heat and cook, stirring frequently, for about 6 minutes, until the shallots are light gold. Add the garlic and cook, stirring frequently, for about 4 minutes longer, until the garlic and shallot are lightly browned.
Stir in the red pepper flakes and the peppercorn-annatto mixture, mixing well. Add the wine, sugar, and soy sauce and continue cooking, stirring, for 1 minute longer. Remove from the heat and let cool completely. This will make a lot more than you will need for making the Lemongrass Chicken. Store the remainder in an airtight container in the refrigerator.
Lemongrass Chicken: In a small bowl, whisk together fish sauce, stock, and sugar until the sugar has dissolved. Set aside.
Heat a wok over high heat until hot; the metal will have a matte appearance and a drop or two of water flicked onto its surface should evaporate on contact. Add 1 tablespoon oil and heat until shimmering but not smoking. Add the chicken and cook, turning occasionally, for 3 to 4 minutes, until lightly browned on both sides.
Remove chicken from wok.
Return wok to heat and add 1 tablespoon oil. Add the onion and cook, stirring occasionally, for about 2 minutes, just until softened. Add the garlic, lemongrass, and jalapeño chile and cook for 30 seconds longer. Add the wine and deglaze the pan, stirring to dislodge any browned bits.
Add the chicken back to the wok. Add the fish sauce mixture, chile paste, and scallions to the pan and continue cooking for 1 minute more, until the scallions have softened slightly and the chicken is cooked through.
Transfer to a serving dish and garnish with the peanuts. Serve immediately.