Okay, here are my 2 yen. No Chabad in Osaka, but there is a nice Shul in Kobe with a Chabad Rabbi. The community became a de facto Chabad of Kansai, but it has a history as a Sephardi community.
If I was in your shoes, I would arrive Wednesday night and take the train from HND to Yokohama. Then early Thursday, go to Kyoto and spend Thursday night and most of Friday in Kyoto. Leave Kyoto for Kobe in time for Shabbat. Shabbat in Kobe, then either Saturday night or first train Sunday head back to Yokohama and switch there to Haneda.
Yokohama is kind of a cool city, but not an amazing tourist stop. I think there is an IHG property there if you need a points stay.
The trains will be more expensive, but way more convenient (and possibly reliable) than the flight and don't require prebooking. You can use Hyperdia to check times. Also google the ANA experience Japan Fares if you're set on flying.