You are right that spelling wasn't standardized until after American independence, on either side of the pond, which is why the differences exist in standard spellings between the U.S. and other English-speaking countries. I should have said "differences in written versus spoken English," rather than "differences in spelling." There isn't that much difference between the written English of Chaucer and that of Shakespeare, but Chaucer is considered Middle English while Shakespeare is (barely) modern English.
The experiment that I posted on this thread --
http://alizeeamerica.com/forums/showthread.php?t=4824 -- shows what I'm talking about. Try to read Beowulf. Then try to read Canterbury Tales. Then (if you can read modern French) try to read Roland. What I found is that both Canterbury and Roland are doable, although very archaic. In Roland, you find "Carles li reis, nostre empere magnes" instead of "Carles le roi, notr' empereur grand," and "qui" is spelled "ki," and there's all kinds of other weirdness, but if you can read modern French you can understand it. In Canterbury, you find "Whan that Aprill with his shoures soot the droghte of March hath perced to the root, and bathed every veyne in swich licour, of which vertu engendered is the flour" -- some words are bizarre, but can't you get the general sense of it? Obviously he's being poetic about "when it's springtime," right? April with its sweet showers has pierced through the droughts of March, and made the flowers bloom. Not so hard.
But Beowulf? Old English? "Hwæt! We Gardena in geardagum, þeodcyninga, þrym gefrunon, hu ða æþelingas ellen fremedon." What the heck is THAT? That's ENGLISH? Getoutahere!
Between Beowulf and Chaucer we had the Norman conquest and the centuries of French-speaking English courts. The difference between those two versions of English represents the traumatic, catastrophic change in the language created by the Conquest. The difference between Chaucer's English and what we speak today, or between Roland's Old French and what you would hear in today's Paris, is the normal evolution of a language over time, absent such a massive event.
You're absolutely right about the methodology questions. How DO we know that Chaucer spoke with a different pronunciation than Shakespeare? For that matter, how do we know how Shakespeare's actors pronounced his plays? No recordings from back then. All we have is the written material. I don't think we can even rely on puns, because these were poets and would do things with language in their verse that they wouldn't normally do talking. So I have no idea how we even know there was such a thing as the Great Vowel Shift. It would be interesting to get an answer to that.