[Elfwreck]

I use Acrobat Pro to edit or convert books for the Reader all the time.

In order of simplicity:
1) Crop
2) Add tags
3) Add Bookmarks
4) Convert to Word, format & reconvert to Acrobat

CROP
When I'm in a hurry, I just crop the pages to remove whitespace. Control-Shift-T opens the crop dialogue; I first go to a page that has the main body of the text so I know I'm not cropping out anything useful. I crop to remove the headers & footers, if any; I don't need the book title & page number showing on the Reader. (It'll show the page number anyway.) It's generally more important to crop top & bottom than sides, because most books are taller than the proportions of the Reader.

So I crop top & bottom to as close to the text as possible, and crop the sides in a little bit but don't worry about how close, because I know there's going to be extra whitespace on the sides anyway.

The crop dialogue will let you crop the current page, a range of pages, or all pages. (I generally crop from page 2 to end-of-book, and leave the cover uncropped.) It'll also crop odd & even differently, if that matters; for published books it doesn't, but for scanned books that's often useful.

TAGS
This will allow reflow to work much better. Most PDFs released by mainstream publishers are not tagged for accessibility, and the reflow in the Sony Reader winds up keeping the original line breaks. (And sometimes, it cuts off in the middle of words.) Adding tags makes it "pre-read" to identify paragraphs, and avoids the worst of the reflow problems.

Tags are found under Advanced --> Accessibility --> Add tags to document. It takes some time (a minute or two is common, longer for very long or complex docs), can double the filesize, and just flat-out doesn't work on some documents, depending on how the PDF was created. Remember to do a save-as, not just a save, after tagging, or the filesize gets a LOT bigger.

Ignore the warnings that appear on the right after tagging, unless you love detailed nitpicky organization work. (Unless you love it enough to spend an extra half-hour for the one PDF, I mean. Manually editing tags is slow and painful work*--worth doing if you're professionally producing PDFs for read-aloud functions, not important for most PDFs for the Reader.)

BOOKMARKS
If I'm likely to read the book more than once, or use it for a reference, I add bookmarks.

Control-B will add a blank bookmark on the page you have visible. Highlighting text first, then hitting Control-B, makes a bookmark on that page, with the highlighted text. (Even if the text is on a different page.)

If there's a Table of Contents, I bookmark that, then use that list to create bookmarks all on that page, then skip to those pages and re-set the bookmarks to the right pages. Right-clicking on the bookmarks gives the option of changing the bookmark location to the current one. (If that didn't make sense, I'd be happy to explain in more detail.)

CONVERT & REFORMAT
If a PDF is just too painful to read full-size, even cropped, and tagging doesn't allow reflow to work well enough, I'll often convert the document.

First I crop to remove headers & footers, because they're easier to remove from the PDF than the Word doc. (Cropping them doesn't actually remove them, but it does keep them out of the conversion.) Then I save the PDF as a Word or RTF file, open that, and start reformatting.

If you like doc formatting, there's a lot of helpful tips I can offer here. If you don't, the quick version involves:

Remove page breaks--manually for a good conversion, by find & replace otherwise (which means you keep some line breaks in the middles of paragraphs)

Finding some way to identify chapter starts, and using find & replace to format those lines, preferably with one of the "Header" styles, so they'll convert to bookmarks when you reconvert.

Select all text; change paragraph to single spaced; change font to 100% size, not expanded or condensed. Potentially change all to a single font of your choice.

Up to you how much you want to search for centered text, which is often converted as heavily indented text, which gets troublesome when you change page sizes.

Change page size: 3.5" x 4.6", or 90x120mm, is about right. (Neither of those is exact.) I use .1" page margins all around; you can play with those settings to your preferences.

I select all text and use the "shrink font" button to reduce it so the main body text is about 10 pt. Then I either manually or with find-and-replace change any header/title text that's insanely big on the small page sizes.

I've set up a "Sony Reader" setting in my convert-to-Acrobat settings; it's got the right page size and shrinks images to 166dpi. I use that.


*Slow and painful, compared to the relatively quick, simple and elegant work of line-by-line proofreading. If you decide to get into manual tag editing, save often and expect to occasionally crash Acrobat. It involves an arcane coding system with almost no useful online help resources.