I have to say I'm quite impress of how good the handwriting search work after converting the pdf... I have a couple of questions and suggestions.
1. Given that you already have the code to convert the pdf into ink wouldn't it be easy to have the option to export to a .one file so it can be opened directly in onenote?
2. It is my understanding that the pdf doesn't have information about the stroke is this right? I'm really surprise that the recognition is so good without this info... Makes you think why is it that Microsoft has refused to implement automatic convert ink in pdfs to onenote's ink. I mean you just showed it is possible and works great.
3. Wouldn't it work even better if you used the stroke information? Perhaps if you used the journal file directly? I think it is pretty much compatible to Xournal http://xournal.sourceforge.net/

I have to say that with this program the Edge has become far more useful. In fact I was even considering getting a HP Slate just for the compatibility with onenote but now there is no need!