Cost, outside of airfare is all up to you. But i don't think any trip is worth it if money is going to cause you to make decisions you wouldn't under better financial conditions.
We went in the spring of '02 but i booked our flights in October, a month or so after 9/11, so each economy seat was only $500 which is great. I was at a convention at Disney of all places and my wife and i met in Chicago for the international flight. It was a sold out flight so we couldn't get an upgrade to FC but ended up getting one on the way back. We flew United if i remember correctly, but just begin checking the various carriers when you are able to book the flights. We had never flown to Asia, but frequently to Western Europe and if you're tall like me, economy is a female dog so i'd suggest getting a small amount of ambien prescribed by your gp. The last thing you want to do when you get there is take a nap and further hurt your adjustment to the new timezone. So sleeping through most of the flight will leave you rested and ready.
I think it'd be a shame to just do TDL/TDS, so try and make it a 10 day to 2 week trip and see Mt. Fuji, Osaka, Kyoto as well as obviously Tokyo and Yokohama.
Hotel Miracosta is by far the best resort at Disney, but think Grand Floridian pricing, so go for any of the tons of hotels that are less than or at $100(10800 Yen right now) in and around Tokyo proper and Yokohama. Disney has a subway stop making staying at Disney as unnecessary as renting a vehicle.
Grab Timeout's(timeout.com) guide to Tokyo. I think their series stomps on the Fodors and Lonely Planets out there.
We were only able to do DisneySeas on our trip, but i'd say 3 days for Disney should get you on all of the bigger attractions and catch most of the shows. Avoid Holidays as weirdone recommends, but realize that the parks are packed all the time as we found out. Just treat the parks the same way you would WDW, grabbing fast passes to Indiana Jones etc right away and then planning your day around those various times.