You can think of these characters as being made up of two parts: A radical that tells you what category of word it is: animals, plants, metals, etc. First up, the two syllabic systems: hiragana and katakana known collectively as kana. Also note that rare kanji also have strange stroke orders, so they may be exceptions anyways.
Examples of jukujikun for inflectional words follow. I remember when I first started learning Japanese and how daunting the writing system seemed.
These sections always come after the parts above them. Kun'yomi are characterized by the strict C V syllable structure of yamato kotoba. In romaji, it may sometimes be ambiguous whether an item should be transliterated as two words or one.
This convention was originally modelled on Chinese writing, where spacing is superfluous because each character is essentially a word in itself albeit compounds are common. This is usually where your first stroke will reside.
Colons and semicolons are available but are not common in ordinary text. This punctuation is also occasionally used to separate native Japanese words, especially in concatenations of kanji characters where there might otherwise be confusion or ambiguity about interpretation, and especially for the full names of people.