Conversion of PDF docs to HTML/CSS

I have 5 50-page PDF docs that need to be converted to HTML/CSS. For each doc, I have the InDesign export to HTML, but we have a specific template for the final HTML. So the project is converting the exported HTML to match the sample section we have already completed. This completed section has all the basic layout and styles in place, so the job is straightforward tweaking of the HTML/CSS, with some formatting and cropping of images, a zoom effect on images, and tweaking of many detailed, data-heavy tables throughout. The PDF docs are being re-written and will become available at about 1 per week. It will be important for everything to be standards compliant and cross-browser.

Finished sample section:
http://msprimers-com.securec34.ezhostingserver.com/section3.html

Sample raw HTML export from InDesign:
http://msprimers-com.securec34.ezhostingserver.com/primer5.html