Score a shallow cross in the base of the tomatoes, then blanch in boiling water and refresh in an ice bath. Drain and peel the tomatoes, reserving the skins in the same bowl. Quarter the tomatoes, scooping out the seeds and inner pulp into the bowl. Place the remaining tomato flesh in a large, deep frying pan. Put the pulp, skin and seeds in an upright blender and purée until liquid. Strain the liquid through a chinois or fine sieve into the frying pan with the tomato flesh.
Cut two large 30 cm (12 inch) squares of muslin (cheesecloth) and lay them flat. Divide the toasted spices, garlic, cloves and bonito flakes between the two pieces and tie using butcher’s string to make 2 flavour sachets. Smash the sachets gently with a rolling pin to bruise the berries and garlic then add to the tomato mix. Place the frying pan over medium heat and bring to a simmer. Add the sheets of kombu. After 20 minutes of light simmering, remove the kombu and discard. Continue to cook the tomato mix over low heat until reduced by half, stirring continuously. Remove the flavour sachets and pass the tomato mixture through a sieve into a clean frying pan or large, heavy-based saucepan and continue to reduce until any liquid has evaporated and the tomato mixture is thick. Season with the fish sauce, vinegar and sugar. Taste and adjust the seasoning to your liking: you want to achieve a balance of sweetness, saltiness and tartness.