In a medium bowl, combine the cucumber, fennel and red onion. In a small saucepan, bring the rice vinegar, sugar, mirin, soy sauce, salt and red pepper flakes to a boil, pour over the vegetables and set aside for 20 minutes (or transfer to an airtight container and refrigerate until ready to use, up to one week). Make the marinade- In a medium saucepan, combine the soy sauce, sake and mirin and bring to a boil. Add the bonito flakes and kombu, simmer for 1 minute, then remove from the heat and set aside to cool. While the soy marinade cools, place the ginger in a fine-mesh sieve over a medium bowl and press down to extract the juice. Pour the juice into the soy marinade, transfer to an airtight container and refrigerate until chilled (the marinade can be covered and refrigerated for up to 3 days).
Strain the chilled marinade through a fine-mesh sieve (discard the solids). Reserve 1/2 cup of the marinade for serving, then pour the remaining marinade into a 10 inch by 5 inch loaf pan. Add the salmon to the pan and marinate for 5 minutes, flipping after 2 1/2 minutes.
In a small skillet over medium heat, toast the sesame seeds until golden and fragrant, shaking the skillet often, about 3 minutes. Transfer to a small plate and set aside.
Remove the salmon from the marinade and place on a cutting board. Thinly slice the salmon crosswise into 20 pieces. Divide the salmon slices among 4 plates and top each serving with some pickled vegetables, shiso leaves (if using), toasted sesame seeds, 2 tablespoons of the reserved marinade and chile oil.
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