Citysuper should have most of the Japanese ingredients you're looking for. It's inside the IFC Mall, which is right where HK Station is. Alternatively, you can go to the food section in the basement of the Sogo Department Store in Causeway Bay.

If you want Chinese ingredients, there are heaps of wet market/grocery stores along Gage Street (near the Central-Mid Levels escalator, ~ 8 mins walk from HK Station).

Regarding the miso paste - If you're flying CX, you can ask the staff for a carton box or whatever packaging that they may have on hand, then check in that additional item (assuming you still have baggage allowance). But it would be best if you can find a box yourself at Citysuper.