Hi Desmond,
Personally I think the Japan Rail Pass is worth buying for you as you are going to be hopping on and off trains as you go across from Tokyo to Osaka on your route. Paying for all those journeys as individual journeys is soon going to rack up. Remember if you are going to buy the Japan Rail Pass then you need to buy it in advance -before you land in Japan. Check with your travel agent re the pricing comparison but I'm pretty sure I'm right. The only time I would say not to bother is if you are landing in Tokyo and staying in Tokyo. Traveling beyond makes the purchase worthwhile as far as I'm concerned.
Disneyland and Disneysea - not cheap but essential when you have little ones hey
Lots to do - and if you do need a break from Disney for a bit there's a great aquarium just one train station away.
Hakone is great - make sure you get on the pirate boat across the lake and take the cable car to a place called Owakudani (it's one of the stations) - and you can eat some black boiled eggs - black because they are boiled in volcanic water. It's great fun and the kids will love it. There's also an outdoor art museum there - lots of sculptures and activities for the kids too. A nice place to relax a little. I wouldn't bother with a tour if I were you - but again that's just me. It's easy enough to get around - just get a good guide book.
Sorry I can't comment on accommodation in Osaka - I live in Tokyo
hence my site name TokyoTopia . Hopefully someone else will jump in there to help.
You'll have a great time I'm sure. I lived in Singapore for a year up at Woodlands.
All the best - Honor