I have a 103 page .pdf document that I need to edit the contents of (change fonts, type sizes, colors, insert revised logos, and place a few style elements). I have the latest version of acrobat pro. that enables you to edit text, but its not entirely efficient. I wanted to load it into ID so that I could create paragraph styles and effectively manipulate the contents of the .pdf. As far as I can tell the only way to do this is to purchase a third party plug in (such as pdf2id)-right? However, the agency who gave me the job, set up a file that looks as though they were able to accomplish my same goal of linking the pdf direclty into ID without the use of the plug-in.
Given the extent of your changes, I think you're in a tough spot.
Even with PDF2ID, there will be a lot of rework to get the file back to where it started, but it may be an option if you can't get the source (InDesign?) file. In my experience with PDF2ID and a 15 page graphics/text document, I ended up with around 100 para styles, 50 character styles, many bulleted sentences missing, images chopped into multiple pieces etc. It took a day to fully clean up, but still better than starting from scratch.
Only other option I can think of is to use the pdf import script 'PlaceMultipagePDF.jsx' to make a 103 page InD document with the placed pdfs as a background, then overlay new content and put images behind transparent areas. Maybe combine this with some pdf edits in Acrobat to remove elements.
Markzware also has released a PDF converter for ID. I've never used it, so I don't know if it works any better.