Tweaked my itinerary a little bit:
OsakaDay 1 Sat: Land at Osaka Kansai airport at night.
Day 2 Sun (OAP): Dotonburi - Hozenji Yokocho - Shinsaibashi - Osaka Castle - Sakuya Kanohona
Day 3 (OAP): Temponzan ferris wheel - Umeda sky building - Museum of Housing & Living - Tenjinbashisuji - Wonder Cruise -
Day 4: Kuromon Ichiba market - Dotonburi/Shinsaibashi - Mameshiba cafe - Shinsekai (evening/night)
Day 5: USJ
KyotoDay 6: Nara Deer Park - Todaiji temple - Naramachi street - Mt Wasakusa hike - brief stroll around Gion & Pontocho Alley - evening/night @ Kawaramachi/Terramachi area
Day 7: Kiyomizudera - Sannenzaka & Ninenzaka steps - Maruyama park - Yasaka shrine - afternoon/evening @ Gion Hanamikojidori/Shirakawa
Day 8 Sat: Hachiman Bori @ Saga - Kyoto Botanical Gardens - Nakaragi path walk - Nishiki market
(Not sure about evening/night plans)Day 9 Sun: Kibune/Kurama half day - Kinkakuji
(Not sure about evening/night plans)Day 10: Arashiyama whole day - Toji temple night illumination
Day 11: Tofukuji - Ginkakuji - Philosopher's Path - Eikando temple
(Not sure about evening/night plans)Day 12: Fushimi Inari - Last minute shopping at Kawaramachi/Terramachi/Gion/Kyoto station
Day 13: Depart for Malaysia

1) Is it worth spending some time at Hachiman Bori @ Saga and at Kurama/Kibune area?
2) I try not to put too many temples/shrines after discussing with SO

Any other places/activities to recommend?

I learnt that if going with womenfolk, must budget time go to shopping malls or shotengais.
Perhaps those empty nites you can fill it with visiting these places.
It wasn't in my itinerary when visiting Nagasaki but I visited various shopping malls & shopping streets much more than I had planned