JR Pass Vs Reginal Vs Individual Tickets

Hey JR Pass team,

Below is a rough outline of a trip I'll be taking on the 26th July - 27th August.

I'd like to know if it'd be more cost-effective to buy JR passes or individual tickets or regional, or a combination of each method, whichever makes the most sense cost wise or for ease.

I understand the JR pass for example includes the boat from Hiroshima to Miyajima return. Also, that I can also use it for taking buses in Tokyo or Kyoto, and that you can get reductions from the pass when visiting certain tourist sites in Japan.

Fly into Tokyo Haneda HND Airport - (26th July)
Train from Tokyo Haneda HND Airport to Minato City District - (26th July)
Sight see in Tokyo - (26th - 30th July)
Fly out of Tokyo via Haneda to Ishigaki - (31st July to 7th August)
Fly into Takamatsu TAK - (7th August)
Travel from Takamatsu Airport TAK to Okayama - (7th August)
Sight see in Okayama - (7th-8th August)
Okayama to Hiroshima Peace Memorial, then to Miyajima (Boat ?), then back to Okayama - (9th August)
Okayama to Kurashiki, then Kurachiki back to Okayama - (10th August)
Okayama to Takamatsu, then Takamatsu to Sanuki-Shirotori Station - (11th August)
Sanuki-Shirotori Station to Tokushima, then Tokushima back to Sanuki-Shirotori Station - (12th August)
Sanuki-Shirotori Station to Kyoto - (13th August)
Sight see in Kyoto - (13th-16th August)
Kyoto to Nara, then back Nara to Kyoto - (17th August)
Kyoto to Osaka, then back Osaka to Kyoto - (18th August)
Kyoto to Matsumoto (19th August)
Sight see in Matsumoto (19th-20th August)
Matsumoto to Kamikochi, then Kamikochi back to Matsumoto (21st August)
Matsumoto to Azumino, then Azumino back to Matsumoto (22nd August)
Sight see in Matsumoto (Onsen etc) (23rd-24th August)
Matsumoto to Tokyo - (25th August)
Sight see in Tokyo - (25th-26th August)
From Minato City District train to Tokyo Haneda HND Airport to fly back to UK - (27th July)

Look forward to hearing from you and visiting Japan - ;-)
Regards
John & Nivi