Assistance on transportation details

We plan to visit Japan in the first half of November for a DIY 8 Nights Itinerary:
Day 1 (Wednesday) will arrive Tokyo NRT around 3 p.m. & stay at Shinjuku Hilton for 4 Nights.
Day 2 (Thursday) Attractions in Shinjuku, Asakusa, Shibuya, Ginza ............
Day 3 (Friday) Tsukiji Fish Market & Yokohama
Day 4 (Saturday) Day Trip to Kamakura, Kawasaki & Kawagoe
Day 5 (Sunday) Travel from Shinjuku to Mt Fuji & Lake Kawaguchi and will stay in Kukuna at Fujikawaguchiko for 1 night.
Day 6 (Monday) Travel from Kawaguchiko to Osaka by Shinkansen (fastest route). Will stay in Swissôtel Nankai Osaka at Namba for 3 Nights.
Day 7 (Tuesday) Day Trip to Kyoto & Nara from Osaka
Day 8 ( Wednesday) Osaka Attractions
Day 9 (Thursday) Leaving Isaka KIX around 10 a.m.

Would the recent Kansai situation affect our Itinerary in the coming November?

Would like to seek advices and assistance for all transportation means. Would JR 7 Days Pass works or other day passes or IC Card or individual tickets work better for our cost efficiency !

Jr national pass wont work.

I would just use single tickets for you long distance travels. And day passes for regions.

Agree with PP that if you do only Tokyo - Osaka but not return, then the 7 day JR pass will not pay off.

Regarding the situation in Kansai, already now EXCEPT for KIX it is no problem here. Yesterday the conbini's were a bit empty of food but today everything is back to normal. The only potential issue can be KIX. So far information is very sparse. While today terminal 2 reopened again, the main problem is how to get to the airport with two of the 3 bridges being heavily damaged. I have not yet seen any forecast by when they can repair them, but if you saw pictures it is a huge repair that is needed. So if you could fly out from Nagoya or Itami to Narita to home that might be a bit safer. However in the end, if KIX remains close you are in about 3,5 h from Osaka in Narita and in less time in Haneda so overall it is not a problem.

You have one day where you have Kawagoe, Kawazaki and Kamakura all in one day as day trip from Tokyo. I assume that the "and" is an "or". There is really no way you could visit these 3 places in one day. Just concentrate on one. If I would need to choose, I would have no hesitation at all to go for Kamakura. (I am not even sure what there is to see in Kawazaki and I dont find Kawagoe so interesting.)

Enjoy your trip to Japan!