Even though it is on a JR train, a portion of the ride from Ebisu to Shin-Kiba -- the part through O-daiba -- is, I believe, on private tracks so there may be a modest extra charge (probably about Y350 per person) charged when you exit at Shin-kiba. I am not positive this will happen since I haven't gotten off at this station lately, but it happens at intermediate stations on O-daiba.

Should you need to return, buy the minimum priced ticket at Shin-kiba just to pass the ticket gate, since your JR pass will let you exit at Ebisu.

If you transit to the Keiyo line by taking that long walk at Tokyo station, there will be no supplement and your JR pass will be good the entire way. There are escalators and some moving walkways.

With bags, you can take escalators most of the way to the Hibiya line at Roppongi, but will have to walk up one flight of stairs at Ebisu. There is an escalator up to JR at Ebisu. Don't know the situation at Shin-kiba, probably some stairs up.

Alternatively, you can take a taxi(s) back to the Keiyo line at Tokyo station. In that case, get the hotel to tell the taxi to take you to the Keiyo line and they should drop you off so that you can avoid the long walk, but might still need to go down one flight of stairs (then there are escalators after that).

There appears to be no convenient bus service. Take a look at

http://www.tokyodisneyresort.co.jp/t...ess/index.html