I have been implementing the yepnope script loader as part of the modernizr.js library. I have successfully got jQuery to load and jQuery dependent scripts afterwards. I am
right before the closing body tag you can be quite sure to be at $(document).ready() state.
What you need to answer for yourself is whether it makes sense to force yepnope to load in a $(document).ready() fashion, as its main purpose is to break the synchronous loading order of script tags in the first place.