Combine the soy sauce, honey, brown sugar, and vinegar and lemon juice in a large bowl. In a mortar, add the habanero pepper, chili flakes, garlic, ginger and thyme, grinding into a paste with a pestle. Add to the soy sauce bowl.
Place the wings in a large plastic bowl and add the marinade. Refrigerate for 8 to 12 hours.
Preheat the oven to 350. Remove the wings, arrange on a baking sheet and cook for 20 minutes. Place the remaining marinade in a small saucepan, bring it to a boil, and then reduce to a simmer, cooking for 12 minutes.
Raise the oven temperature to 400, brush the glaze on the wings and cook for about 20 minutes. Remove to a platter to serve.