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Early modern English, as with most European languages, had T-V distinction. That is, there were two versions of the word "you": "you" (formal) and "Thou/thee" (informal). It became customary to address God in the "thou/thee" form, and when thou/thee was abandoned by most English speakers, the fact that many addresses to God were presented in "thou/thee" form made them think that thou/thee were old formal terms (though the reverse is true).
In Early Modern English, some conjugations are different from present use. For example, Early Modern English "hath" would be translated today as "has."
See Modern English for more information on English as it used from 1650-present.