Travelling Through Japan

Hello,

I generally wanted to see what the best alternative travel, or see if I need the Japan Rail Pass. What train stations I need to get to, etc.
So, basically, we are taking a tour starting from Tokyo and ending in Osaka.
Since we are ending in Osaka we plan on extending our stay in Toyko for a few days.

We want to:
- Travel from Osaka back to Toyko. - Going to Toyko Disneyland. - Then eventually travel around locally around Toyko via train stations - Then from Toyko back to Haneda.

What should we do, or the easiest/most affordable options!?