In a food processor, puree cilantro, coarsely chopped onion, garlic cloves, jalapeno peppers, stems removed, 1 cup naranja agria (sour orange juice), or ½ cup fresh orange juice plus ½ cup fresh lime juice, achiote paste and Kosher salt.
Place chicken in a resealable bag or large bowl and pour marinade over; turn to coat. Seal bag (or cover bowl) and chill at least 4 hours and up to 1 day.
Prepare a grill for indirect medium-high heat (for a charcoal grill, bank coals on one side of grill); rub vegetable oil on grill grates.
Remove chicken from marinade to a large platter. Letting any excess marinade drip back into bag or container. Season chicken lightly with salt.
Prepare a grill by preheating to 450 degrees. Oil the grates using vegetable oil.
Once the grill is heated, turn down to 350 degrees and turn off the middle station to create a cool zone. So you'll be cooking over indirect and direct heat.
Place chicken pieces on oiled grill grates, and place the chicken pieces on the grill. Place chicken thighs skin side up. Grill chicken for about 10 minutes with lid closed.
Turn the chicken and start moving the chicken around every few minutes, utilizing the cool zone for any pieces that have become too charred. Keep the lid closed as much as you can.,
Cook chicken until an instant-read thermometer inserted into the thickest part of thighs registers 170°, a total of about 30 minutes.
Transfer chicken to a cutting board and let rest 10 minutes before serving. Serve with lime wedges for squeezing over the chicken.