Please keep in mind that I won't be driving. It'll all be walking and train routes for us. PIONEERS!
...Anyway...
Are you sure there will be limousine buses bringing people anywhere they need to go from the Narita airport? It was my understanding they just transport you to the Hilton hotel... or something... Also, how would we get back to the airport from Yokohama? Would there be limousine buses at the hotel to take us back to the Narita airport? We'd probably stay in the Sakuragicho Washington Hotel. It's the cheapest and it's close to both locations.
With the transportation to/from the airport/hotel down, let's focus on Midoriyama. Shinjuku seems rather out of the way if I'm staying in Yokohama. So, from the Washington hotel, what would I do?
I tried reading the information you gave me, but there's one major flaw in the site's system. I can't translate the PICTURES to English. :P
All I could figure out from the information you gave me and Google Earth is that I'd need to get on some line in Yokohama (don't even know the station I would need to go to) and I'd have to end up at the Nagatsuta station. From there, I'd have to take the Kodomonokuni line to the Kodomonokuni station, where my train adventures would end and I would take a bus, hail a cab or maybe even just walk.
Then, coming home, I'd... um... I guess do everything in reverse?
As for Muscle Park... I haven't even tried. My head already hurts.