There really is no right or wrong answer here - you should do what you have the stamina for, and go to places that you are interested in. Going straight from Narita to Osaka would be piling on 4 hours of train travel on top of just getting off of a long airplane trip - so that is not my idea of a relaxing trip. But maybe you prefer things that way.
Honestly though, because you are already seeing Tokyo, you can mostly skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori.
On another evening, you could also go and see Kobe.
Instead, you might want to go visit Himeji, with Japan's best castle. The Kokoen Garden next door is also beautiful.
I suggest you look at the official city guides on the places you mention:
Good luck.