EDIT: Eiríkr Útlendi has answered my question mostly in regards to readings. What remains is how kanji are chosen for their meanings and why certain words are selected over others e.g. 実 versus 果実. Also there are exceptions to the rule e.g. 天竜人{てんりゅうびと}. How do those factor in?
I've been watching the Anime "One Piece". There are quite a few compound words that obviously seem made up for the universe, and when I look them up the constituent kanji either don't follow the readings they would as original words [example 1] or they use a listed reading that doesn't occur in any words I can find in my dictionaries [again example 1] (I use ejje and Jisho). Otherwise, there are words that use readings that appear more archaic or irregular to me [example 2 and 4]. Then there are words that use the kanji and readings of the original word (in example 3, "emperor"), but only part of it (in this example, only one of the kanji of 皇帝 and thus only the reading from one kanji). Maybe my vocabulary is too poor and I'm making mistakes because of that, but here are the examples:
Example 1: 三{さん}刀{とう}流{りゅう} Translated as "three sword style" - This makes sense, except why is とう and not かたな used?
Example 2: 海{かい}楼{ろう}石{せき} Translated as "Sea Watchtower Stone" - 2nd makes sense, but I don't understand why かい is used for the 1st and not うみ and せき (I can't find any words with this reading) instead of いし for the 3rd.
Example 3: 四{よん}皇{こう} Translated as "4 emperors" - Why just こう and not よんこうてい
Example 4: 七{しち}武{ぶ}海{かい} Translated as "7 Warlords of the Sea" - Here かい again. Also why use the irregular reading しち?
Example 5: ゴムゴムの実 Translated as "Rubber Rubber Fruit" - Why not 果物 or 果実?
Is there a logic to these? Are they just made up to sound cool? If so, how will I know when reading a new manga what these made up words mean? Someone can definitely tell me that I'm overthinking this, haha.
Thanks for your input.