Hold the tail tube portion of the squid and with fingers, grasp the cuttlebone (the thin, clear cartilage inside the tube) and pull from the squid's body.
Remove black ink and discard. Wash the squid and drain well.
In a bowl, combine honey, brown sugar, vinegar, garlic, ginger, salt, and chili peppers. Stir together until sugar and salt are dissolved.
Gently add squid in a single layer. Cover and marinate in the refrigerator for about 1 hour. Drain squid very well and thoroughly pat dry. Reserve marinade.
In a saucepan, boil the reserved marinade for about 7 to 10 minutes or until reduced.
In a bowl, combine tomatoes and onions. Season with salt and pepper to taste.
Divide tomato-onion mixture and stuff each of the squid.
Grill squid over hot coals for about 4 to 5 minutes on each side, regularly basting with marinade.