Have you looked into flying from Takamatsu to Haneda? I would probably do that over a pass, since it will likely shorten your trip by quite a bit. It's 330 minutes from Takamatsu to Tokyo (and taking the ferry to Uno and traveling to Okayama is not going to save you a lot of time because there is almost always a 30-45 minute layover in Uno, so you can just as easily go to Takamatsu.) Heck, when I put Takamatsu to Tokyo in Hyperdia, I still get flying from Okayama to Haneda is going to be faster than taking the shinkansen because you can only use the less frequent Hikari (and Sakura if you want to change by Shin-Osaka or before) and can't use a Nozomi. And by the time you are paying out of pocket as a foreigner, it should be cheaper to fly using one of the discounted JAL/ANA fares than to take a Nozomi.
If it were me, unless there is a specific reason to do Osaka before Kyoto I would do:
Tokyo 3 days
Tokyo to Kyoto Kyoto 5 days and pay out of pocket for a Nozomi
Osaka 5 days
Osaka to Naoshima via a Kansai Wide Pass: https://www.westjr.co.jp/global/en/ticket/pass/kansai_wide/
I would start it during your time in Osaka in case you want to do any day trips that would be covered by said pass and end it on the 5th day with your trip to Naoshima
I would then fly from Takamatsu Airport to Haneda Airport
So you would have as travel costs: ~14,000 yen Tokyo to Kyoto
9200 yen for the Kansai Wide Pass
and 10,000 yen for the airfare for a total of 33,200, which is much less than a 2 week pass
The Kansai wide Pass would give you flexibility if you want to make some day trips from Osaka, like Himeji.
Rail Passes can be a good deal, it really depends on how much you are traveling and how you are traveling and which lines you are using. The less long distance traveling via shinkansen you are doing in a given time period the less it is worth it. I like the rail pass, but it does really hurt you on the Tokkaido line between Tokyo and Hiroshima, because the majority of those trains (I want to say 5 every hour) are Nozomi or Mizuho which can't be used with a pass. There are only 2 Hikari an hour and usually 1 Kodama. Kodamas are fine if you are going to a smaller shinkansen station or just want to spend hours sitting on a train, but they do take much longer than a Hikari. It's ~135 minutes by Nozomi between Tokyo and Kyoto, 158 minutes by Hikari and more like 225 minutes by Kodama!