Since I'm a broke student I use Evernote free. I converted some of my journal notes to jpg once for Evernote and was able to search for words within them, so I'm not sure why it's not working for you.
Oh - I see now - it does OCR PDFs but not yet handwriting
http://forum.evernote.com/phpbb/view...17733&start=25
so you can, if its important enough, convert your PDF notes to JPG then add to Evernote. On March 4th it was posted it is to be deployed soon.
Cool PDF viewer - free and portable to convert
http://www.pendriveapps.com/software...rd-processors/