Combine salt, cayenne pepper, garlic powder, cumin, Mexican oregano, and thyme in a spice grinder until powdered. Set rub aside.
Combine beef, almond flour, bell pepper, onion, jalapeno, egg, and garlic in a bowl. Mix lightly with hands until loosely combined. Gently fold in spice rub mixture until distributed throughout.
Punch holes in the bottom of the aluminum foil pan and coat with grapeseed oil. Form the meat mixture into a loaf and place in the prepared pan. Place in the refrigerator to chill while preparing the smoker.
Preheat the smoker to 250 degrees F (120 degrees C). Place a water-filled pan under the grate where the meatloaf will be placed. Fill firebox with charcoal and 1 chunk pecan wood.
Place meatloaf in the hot smoker.
Combine apple juice, vinegar, bourbon, water, Worcestershire sauce, and lemon juice in a clean, all-purpose spray bottle. Spray the outside of the meatloaf well with apple spray every 30 minutes.
Refill firebox with charcoal and 1 chunk pecan wood every 45 minutes to maintain temperature; ground meat absorbs smoke very easily, so use only 1 chunk of wood at a time. Smoke meatloaf until internal temperature reaches 130 degrees F (55 degrees C), about 2 hours.
Combine water, ketchup, vinegar, Worcestershire sauce, paprika, mustard, lemon juice, honey, liquid smoke, ancho chile powder, red pepper flakes, and black pepper in a saucepan over medium-high heat. Bring glaze to a boil and reduce to a simmer. Cook until reduced, about 20 minutes.
Discontinue apple spray; brush glaze over entire top and sides of meatloaf every 30 minutes. Continue smoking until internal temperature reaches 160 degrees F (71 degrees C), 4 to 5 hours more. Remove meatloaf from smoker and let rest 10 minutes before cutting and serving.
