This type of problem in spelling is also addressed by Stanley Wells in Re-editing Shakespeare For the Modern Reader:
"G. Blakemore Evans has provided additional examples of problems arising from 'the use of a common single spelling form for words of different meaning': thus, 'loose' and 'lose'...'of' and 'off' are, as he says, all confusible; so are 'cheerly' and cheerily', and we may be uncertain whether 'farre' means 'far' or 'farther.'"
There is also a question of the ambiguity that is intentional is some of these spellings. Many times there is no distinct meaning that should be taken from a word, but the word in its idiosyncratic spelling is supposed to suggest multiple meanings for a word. This inherent doubleness is part of what this web tries to simulate for the reader.