If you have access to the source, why not add that directly to Calibre and let Calibre do any conversion?
I think you should be able to remove the ABC strings from a PDF file by using the facilty in Calibre for removing headers/footers. However you would have to create the correct Regex expression for reognising them for this to work.
Also as someone mentioned if you have a paid-for version of the ABC PDF converter (rather than the demo version) you can stop these watermarks being output.
Last edited by itimpi; 12-20-2009 at 08:31 AM.