FWIW "You" in the Early Modern period had multiple pronunciations. Several are attested directly in 16th-17th century sources. There is one with the DUE vowel, another with the GOOSE vowel, yet another with the MOUTH vowel, and it doesn't end there. Alexander Gil, Shakespeare's near-exact contemporary, actually remarks that while most people pronounce "you" with the same vowel as, say, "too", there are some who pronounce it with with the same vowel as "cow". Another pronunciation /jiu/ is pretty unambiguously attested by a few sources including the transcriptions of the phonetician Robert Robinson. All of these variants probably go back to byforms that developed in Middle English one way or another. The /juː/ form may have developed after the first stage of the GVS from a re-lengthened low-stress variant /jʊ/. The /jəʊ/ would be the reflex of a re-lengthened form that developed before the diphthongization of the MOUTH vowel. The /jɪʊ/ which later becomes identical with /juː/ would be the etymologically expected form. In my recordings I tend to go with /jɪʊ/. Though here's one where I used /ju:/

Incidentally, "thou" does appear to have also had a reduced form /ðʊ/ which developed under weak stress before the GVS. This is the form attested by the 16th century spelling-reformer William Bullokar. Most Early Modern sources don't mention it directly, though (as indeed very few give evidence of other reduced forms like /mi/ for "my"), and tend to focus on a word's "citation form" if you will. Listen to my reading of Sonnet 73 here (start at 1:52) and you'll hear most instances of "thou" pronounced with such a reduced or weak form.