Pass type advice requested on Tokyo/Osaka & area travel

Hello! The Japan transit system seems intuitive, but its pass & card system feels impenetrable.

I will be travelling to Japan for the first time soon and plan to be making the following trips on my itinerary. What sort of JR pass, transit card, or combination thereof would be the most efficient and cost-effective for this list of station-to-station transit? Please forgive any inaccuracies in station names.

Day 1 (Tokyo area):
Haneda to Shinjuku

Day 2 (Tokyo area):
Shibuya to Ochiai-minami-nagasaki
Ochiai-minami-nagasaki to Shinjuku

Day 3 (Tokyo area):
Shinjuku to Tokyo Teleport
Tokyo Teleport to Shiodome
Shiodome to Tokyo Station
Tokyo Station to Akihabara
Akibahara to Shinjuku

Day 4 (Tokyo area):
Shinjuku to Kichijoji
Kichijoji to Keio-Tama-Center
Keio-Tama-Center to Takaosanguchi
Takaosanguchi to Shinjuku

Day 5-17: N/A (on tour)

Day 18 (Osaka area):
Kitashinchi to Osakajokitazume
Osakajokitazume to Itami + bus
bus + Itami to Iga-Tetsudo
Iga-Tetsudo to Osaka

Day 19 (Osaka area):
Osaka to Arimaonsen
Arimaonsen to Shin-Kobe
Shin-Kobe to Kencho-Mae
Motomachi to Osaka

Day 20:
Bullet train to Tokyo

Day 21:
Shinjuku to Shin-Yokohama
Shin-Yokohama to Takashimacho
Ishikawacho to Shinjuku

Day 22:
Shinjuku to Haneda

Thank you for advice on this complicated question!