I made a lyrics website for obsessive Joanna Newsom fans: http://www.joannanewsomlyrics.com/.
You can compare different versions of a song: http://www.joannanewsomlyrics.com/compare/12-clam-crab-cockle-cowrie_as_sung/39-clam-crab-cockle-cowrie_as_sung/
You have the choice of seeing the official lyrics for a recording or the "as sung" lyrics. For the official lyrics, I've gone through and made sure they exactly match what's in the booklet.* The "as sung" lyrics are for when you want to sing along — every word is as accurate as I can hear it, nothing left implicit (like "x2" or [chorus]).**
One interesting thing I've noticed so far is that the official lyrics from Milk-Eyed Mender are in many cases closer to what she sings on Yarn and Glue/Walnut Whales than to the Milk-Eyed Mender version.
*No support for italics or special indentation yet.
**I leave out non-verbal sounds like Os, Ohs, and Oohs.