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5
Generally it is not possible to predict whether 町 is read as まち or ちょう.
大手町 at the center of Tokyo is read as おおてまち while there is [大手町]{おおてちょう} in Kishiwada city of Osaka (source).
As mentioned in the link, ちょう is more common in Western Japan whereas まち is dominant in Eastern Japan.
4
In modern Japanese, 種 as a counter for kinds/species is always read しゅ. 3種 is さんしゅ.
くさ is an archaic counter that is no longer in use. You don't have to remember it unless you are studying archaic Japanese literature seriously.
3
As Eddie Kal has mentioned in the comments, you might want to take a look at on'yomi and kun'yomi. However, for this case in particular, はる meaning spring is always written as 春. 陽 is a nanori when pronounced はる, meaning it is usually only pronounced that way when used in names. It is typically pronounced ひ (kun'yomi) or ヨウ(on'yomi). The kanji is used in ...
0
It's not an online resource, but the book よく使う順 漢字2200 presents the kanji in frequency of use order and lists some of the most common words for each.
https://www.amazon.co.jp/%E6%97%A5%E6%9C%AC%E8%AA%9E%E5%AD%A6%E7%BF%92%E3%81%AE%E3%81%9F%E3%82%81%E3%81%AE-%E3%82%88%E3%81%8F%E4%BD%BF%E3%81%86%E9%A0%86-%E6%BC%A2%E5%AD%972200-%E5%BE%B3%E5%BC%98-%E5%BA%B7%E4%BB%...
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