There is not and never will be a single method that always works for doing any alteration or conversion of all PDFs, period. Attempting any such action will always be a matter of trial-and-terror.
That said, I would suggest you start by getting Abode Reader (free) and a PDF virtual printer (aka "print to PDF" software) and give them a try. There are a number of such virtual printers available. I use PrimoPDF
, which is available free, as my PDF virtual printer.
The virtual printer software installs as a "printer" on your system allowing any application that can print to generate a PDF by simply printing to the virtual printer.
Try opening your big PDFs in Reader and then printing to the PrimoPDF (or whichever you get) "printer". Experiment with the settings in PrimoPDF to see which yields the best compromise in file size and image quality.
I've successfully used this method to resolve issues with some complex layered PDFs that contained scanned backgrounds layered behind scanned text. The results were somewhat smaller and performed much better in the reader.