I scanned the pages using my old reliable Epson Expression 636 flat bed scanner with a really nifty Silverfast scanning program to feed images to Photoshop 7.0. I set the Silverfast program to scan the pages at 150 pixels per inch, use it's unsharp masking capability, and "levels" utility to produce good-quality 24-bit color images in Photoshop. Once I have a number of text pages scanned I save the scans as JPEG medium quality and then use Photoshop's Save for Web tools to produce very small B&W GIF format files to use later in Microsoft Word 2002.
Pages with half-tone images take a little more work. I scan those at 600 pixels per inch to capture the dot structure without a moiré pattern. Then in Photoshop I select the half-tone image and use a 2 pixel wide Gaussian Blur filter to produce a continuous tone image by smearing the dot structure. Then I use Photoshop's levels tool to adjust the image shadow, highlight, and image gamma. Finally I resample the large 600 PPI image down to 150 pixels per inch, apply a little unsharp masking and save it as a JPEG medium file to use in Word and Acrobat.
Then I compose a Word document with the JPEG (for photographs) or GIF images placed one on each page. After saving the Word file I use Acrobat's Word plug-in to produce a PDF version of the Word document.
One would think that this is all that is necessary. However, Acrobat adds extra file space when converting Word imbedded JPEG images to PDF. In the case of the GCTA Manual this balloons the file size from 3.5 MB to 5.5 MB!
To reduce the 'wasted' file space I replace the converted JPEG PDF pages with the original JPEG files in Acrobat. That reduces the final PDF file size to very close to the Word DOC file size. The only drawback is slightly different look on the PDF screen display. However everything prints out just fine. Take a look at the file with Acrobat and you will see the difference.
Why didn't I put the GIF files into Acrobat directly? Because GIF's have no print size flag! GIF's placed in Word files and converted to PDF have the size flagged! It took me many tries to work up the most efficient way to produce very readable and printable PDF documents. But the effort was worth it.