1. Via Napoli in the Italy pavilion at Epcot is very good. Allears.net can provide you with the menu. I'd recommend you decide where you want to eat as soon as possible, because restaurants book up super fast and your trip is approaching quickly. Here is an article about Via Napoli from the Disney Food Blog.
http://www.disneyfoodblog.com/2010/0...poli-pictures/
2. You will have a fun time visiting the Wizarding World of Harry Potter. I'm a big Harry nerd also. The area of the park that it takes up is really not very big so don't be expecting a huge land. The Forbidden Journey ride inside Hogwarts is fantastic! Aside from that, the few other rides they offer in the area lack great theming, but it is fun to walk the streets of Hogsmeade. Don't forget to enjoy a glass of Butterbeer! I have heard that they plan on expanding this portion of the park, so hopefully they really enhance it and convince me to visit again.
The Spiderman ride at Islands of Adventure is also a lot of fun.
3. I was in Disney from January-June last year and my family just so happened to visit me the week that you will be there this year so hopefully I can give you a decent prediction of crowds. I think your 90 minute guess for rides like Space Mountain, Rockin' Roller Coaster, etc. is probably pretty accurate. Things like Soarin' and Toy Story Mania will be even longer. I recall Small World and Haunted Mansion having 30-40 minute waits during that time...which is fairly long for them. That said, since there are only two of you and no kids, hopefully you will be able to cover ground fairly quickly. I'd recommend getting to the parks early and you will probably be able to get a lot done. Also get your Fast Passes for the major attractions early, because they will run out for the day.
4. I recall having a few days of rain during that season last year, but for the most part it should be nice. And if you do get stuck in the rain, it means the park will be empty so that is a plus side. Temperature wise it will probably be very nice.
5. You can either connect from any of the parks to the Transportation & Ticket Center to catch a bus to DTD or you can take a bus to any of the resorts (every Disney resort will have its own bus stop at all of the parks) from the park and then connect to DTD from the resort. I'd recommend the resort option just 'cause it's more fun. If you're wanting to go to DTD after leaving MK, take the monorail to the Contemporary, Poly, or Grand Floridian, then catch a DTD from there. You can also bus to Saratoga Springs or Port Orleans from any of the parks and then take a boat to DTD, which is a nice and relaxing ride. And yes, the transportation is free.