There are so many variables involved in why you sometimes run into problems exporting a book w/lots of placed PDFs into one big PDF, it'd be really hard to diagnose. I guess I'd look at RAM first, and then perhaps reducing the PDF file size in Acro before you place it/them. I'm also wondering if fonts and font subsetting are a problem. You know when you place a PDF and then export to PDF, InDesign is essentially “re-frying” the PDF again, and thus has to re-subset all those fonts. I don't know of any surefire fix for avoiding font conflicts/problems other than rasterizing the PDFs in Photoshop first (changing them into pictures) before placing into ID, and that would be probably be a last resort.
You can insert dividers (extra pages) into an InDesign file, but you'd have to manually create a new section with a new starting number for the “real” doc page following that divider so that the divider page isn't counted. So if you have a 10 page doc and insert a divider page after page 5, you'd go to page 7 (the first page after the divider), choose Numbering and Section Options, turn on Section Start and Start at Page Number and enter the number 6. In the document, the Current Page Number special character will honor what you set here.
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