"you" versus "You" as polite form of writing
Is it correct to write "You" with a capital Y as a form of politeness? If yes, should I use that form throughout the entire letter/document, or only at specific places?
Solution 1:
No, it would be seen as unusual, perhaps archaic. The only reason I is capitalised is that i doesn't stand out visually, and needs added visual emphasis. He, Him, and His are capitalised when referring to God (or variations thereof) in Jewish, Christian, and Islamic texts. In that context, You and Your (or more typically Thou, Thee, Thy, and Thine) would also be capitalised.
Certain titles such as Her Majesty the Queen also include capitalised pronouns, but simply because they're titles, like Doctor or Professor.
Solution 2:
Capitalized pronouns in English, besides "I", are invariably used to refer to some higher power, most often the God of the Judeo-Christian faiths. The only other proper usage of capitalization of pronouns is in titles.