Well, your are getting ahead pretty nicely. You may even beat iRex
I have included a picture of a sketch I made, and the resulting "merged" PDF from the iRex PC application... judge for yourself. Anybody had better luck?
I have also included a zipped folder with the default MeetingNotes.pdf, the 1024x1280 Blankpage.pdf I made and properly "templated" (the one thing that actually works in the PC app) and BlankPage 001.pdf, which contains 5 more or less vertical and 5 horizontal lines, one each for every pen size. (plus the corresponding metadata.db) Maybe that will still help in the decoding. I deleted the .db file just prior to doing the test, so this one should be spot on.
I lost the .db with the sketch when I was playing around with files. Definetely, the drawing contained in the metadata will be applied to simply any PDF with the corresponding filename, even if the content has changed.