Nishiki market is generally closed on 31 Dec and opened from 4 January onwards.
https://m.chiebukuro.yahoo.co.jp/detail/q1420025139?query=錦市場+年末年始
Malls should be opened on 2-3 Jan for fukubukuro (lucky bags) sales. Individual shops (not all) should be opened from 2 Jan onwards.
Updated itinerary.
hiroshima and miyajima will be skipped if not getting JR pass
31st will stick within Gion area for countdown. nishiki market will be open till evening if im not wrong, if not can be skip.
21 07.30 arrive NRT
22 nakano boardway, ikebukuro
23 akihabara, odaiba
24 tsukiji,ginza,ueno(ueno park,ameyoko),asakusa(sensoji,Asakusa Underground Street),skytree
25 shinjuku,harajuku(Meiji Shrine,takeshita dori),shibuya(Shibuya Crossing & Hachiko Statue)
26 namba,dotonbori,shinsaibashi
27 osaka
28 osaka
29 *Hiroshima(Hiroshima Peace Memorial Museum(close on 30)
30 *Miyajima(stay one night or go kyoto)
31 Gion,potocho,Nishiki market
01 Arashiyama
02 Fushimi Inari
03 Kiyomizudera
04 kyoto ->Nagoya(shinkensen)(stay one night)
05 Hida takayama / Gero(stay one night)) (Hida Wide View Express train)
06土 Hida Furukawa,Shirakawa-go (stay one night)
07日 kanazawa(Stay one night)
08月 kanazawa-> tokyo (Hokuriku Shinkansen 2hr30min)
09火 hakone or stay at tokyo
10水 hakone or stay at tokyo
11木 disneysea
12金 tokyo roppongi,akasaka sacas
13土 tokyo last day shopping
14日 08.50 HND depart