First, notify a mod to move this thread to Japan forum so the experts there can give their input.

Since you are doing open jaw, you don't need a Japan Rail Pass.

I would spend the first night in Tokyo just to see how jet lag is affecting you. If you stay near Ueno/Asakusa area it will be easier to take Tobu train to Nikko on day 2 (maybe buy the All Nikko Pass.) Keisei Skyliner/Access Express is more direct to Ueno than Narita Express.

Nikko can be done as a day trip or you can spend a night in an onsen ryokan and return on day 3.

I think the rest is fine. How much time you want to spend in each city should be decided on what sites you want to visit.