my last 3 trips (once last year and twice this year) to Japan was by ANA. its a full service flight like others. nothing special about their food, i liked the JAL ones better. I don't really like night or overnight flights due to lack of sleep, so the timing of their Narita flight suits me although i waste almost a day. the plane is the latest 787 dreamliners, which JAL now has as well. the toilets are fitted with auto-bidets as well. seating is 3-3-3 in a row. special drink on board is kabosu juice(lemonade) , whilst JALs is Kiwi sky juice.
service-wise ANA and JAL almost equivalent. i havent took MAS for a long time already whilst i always try to avoid Air Asia(because i don't buy early bird tickets as i usually plan my Japan holidays according to announced Nogizaka46/AKB48 idol events and concert tickets availability; Air Asia tickets bought late and full service flights pricing almost the same)

you usually can see some form of Sakura during that long period esp in Tokyo, Nagoya, Osaka, Kyoto.
as to what stage of bloom depends on weather, temperature and location. if the winter is very cold and long, the blooming may start later and takes longer to reach full bloom(in which case, the somei yoshino blooms may be more pink than white). if the temperature gets warm pretty quickly, the full bloom is reached quickly (then, it may be more white than pink). also the location plays a part, such as Ueno park is one of the places where it starts blooming a few days earlier than the others. once it reaches full bloom, humidity and weather/wind plays a part on how long the bloom lasts. if it is rainy and windy, chances are the petals may wither quickly and the bloom just last a few days, then the sakura trees will look like a normal green tree.

your area is pretty troublesome to travel to, despite Tokyo trains run pretty late.
you'll need to rush, but before that , you'll need to clear immigration and customs and find your way to the train station.
hyperdia.com is your friend when travelling by rails. very accurate with many options. Japan's transportation are pretty punctual, there could be delays but they have a catch up system to ensure they are not too late.
i got another website that teaches how to travel by bus as well, but its in japanese so for a start, use hyperdia.

those going to Japan in the next few days, there's an abnormal typhoon coming. its over the Japanese TV stations news now and then as it approaches inland. if you go to the official meteorological website, you'll also see it . so do take care. check your airlines for delays and postponement. also, trains and railways may also be stopped or have limited service.
http://www.jma.go.jp/en/typh/1705.html