I haven't stayed at the Hilton, but it sure looked nice from the train! I'm sure it'll be pretty nice.
2 days at each park sounds great! I only had one day to cram in both, but it was also just me-- no kids or hubs to worry about
I do have one in-park recommendation: there's a Japanese restaurant in the bazaar area of Tokyo Disneyland (their Main Street USA equivalent) that has a katsu that straight-up melts in your mouth. I was really impressed. (I ate there because my coworkers were so whiny about eating Japanese food! They wanted like one sushi meal-- no ramen or curry or anything. Boooooo.)
The two-store thing at Ikspiari threw me off! One is sort of just the Japanese equivalent to the American
Disney store-- lots of merch, and it's not specific to the park per se, but it's stuff you won't be able to get outside Japan. (If you plan to go to the big Disney store in Shibuya, it might have the same or maybe even more stuff-- I haven't been there.) There's a SECOND store that's just past Ikspiari, about a block's walk past the Maihama subway station, that is a giant store that has more park merchandise...at least, that's how it was explained to me. I didn't have time to explore that store because I was rushing to get to the airport, I ran in just long enough to see if they had any Chandu merchandise (they didn't!) and then left. There's also a bunch of other mid- to high-end shopping at Ikspiari, including an Ippudo if you want to check out one of the bigger ramen shop chains in Tokyo, it's pretty good for a chain.
(Hyper-specific tip: If you are/fall in love with Chandu, the adorable tiger from the Voyages of Sinbad ride, buy his merch at the shop closest to that ride...there's not much else in the parks, maybe nothing else.)
One other super random tip...they do NOT have coin-op lockers
inside the parks like they do at the American parks, so there's nothing (for example) right next to Splash Mountain. If you wanna do a water ride and don't have a designated non-rider to hold electronics, you may want to think ahead about bringing plastic bags to protect them or putting them in the lockers outside.
Sorry, now I'm blathering. I loved the parks so much when I visited for that one day! You're going to have a blast!