1. do "sketch -> add file" twice, first on PGraphicsPDF.java, then on itext.jar from the libraries/pdf. or just drag each file to the sketch editing window to do this automatically.

2. remove the package designation in PGraphicsPDF, and give it a new class name, but keep the tab name ending with .java, ie MessyPDF.java

3. now hack away with pdf it as you please. size(500, 500, "MessyPDF", "output.pdf") or whatever.

there are two things at work, one is that itext will clip things by default to the main area, so removing the crop area in illustrator will sometimes reveal overlapping bits. sometimes it also clips out to reduce file size if it's off screen. but these may be things that you can shut off. personally it sounds like a mess and that you might instead want to just scale() your sketch smaller so that everything is included, then clip later.