Hi, @jampff, first off, it sounds like you've done an impressive job working against a temendous challenge.
Let me try and explain how Acrobat is not meant for extensive editing. Acrobat is a digital print, first and formost. Its strengths include that a PDF document can be opened on just about any platform and look like it's creator intended it appear. In addition, it can have fields that can be filled out, it can have regions for leaving signitures, and with long documents, you can split it into pieces, extract selected pages out of the original, and many other important functions.
The PDF format is so successful and so important for world digital activies, that Adobe GAVE UP the rights to the PDF format and it is now a world wide ISO standard. Any changes that are made in the PDF format have to be agreed upon by the ISO International Committee. That's big time. Adobe, Apple, Microsoft, and many other 3rd parties write code to read, and edit (to some limited degre), and some of them follow the ISO guidelines (and no, neither Apple or Microsoft do a great job of following those guidelines. They do OK, but not great).
Did you know you could write a book in Photoshop? I can't imagine anyone wanting to, but you could. After all, you can type, you have access to all the fonts on your computer, Tab features, Centering, Left and Right allign; all in all, it can do impressive layout. But, it would be sooooo much more work than using just about any other Adobe application outside of Illustrator. Just thing, no automatic page numbering, no word-wrap around objects and no word-wrap from page to page. That's just a few of the things you cannot do when writing a book in Word.
Many years ago I wrote a book, and at that time, I used Microsoft Word. It was horrible, but at that time (mid 80s), but it sorta worked. When it came time to write the next edition, I used FrameMaker for the Mac. It was amazing and fantastic. It was hard — my joke was that FrameMaker should be given away for free, but the manual was $900 — since it was impossible to figure out how else to use it. But I saved so much time becuase it was a proper page layout application.
There are two primary writing applications: text-intensive applications like Word, or page layout applications like FrameMaker and InDesign. With the latter two you can have word-wrap around objects, consecutive page numbering, consecutive section numbering, consecutive figure numbering, etc. Yes, you can do some of that in Word, but also you can do that in Photoshop via manual setting for each one.
I'm sorry to belabor all this, but you spent a long time asking a very important valid question and I'm trying to give you the best explanation I can. The code for what can be done in a PDF is very focused and very limited. It's much better than what can be done using Whiteout on a Typewriter, but for best service, you should think of Whiteout functions when "editing" in Acrobat.
Maybe sometime in the future, Acrobat will work just like Word or InDesign, with functionality of Photoshop and Illustrator. But I'm pretty sure that that program would be very slow, full of bugs, and a real pisser to use. But, if you want to see development, try using Acrobat 2 — that's what I started with. (LOL)
Anyhow, all this is to say that the BEST way to edit a PDF document is to open up the original application that made the document. If that is completely not possible, save the document into a Word document, fix all of the wierd formating things that will need to be fixed, do the editing you want/need, and then resave it into a new PDF.
I'm sorry this is not the answer you were hoping for.
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