How many different layouts do you need for one report?
I can think of two. Portrait and landscape.
I know everyone expects to have multiple layouts like ArcView 3, but there are equivalents.
You can export pages into one print document at the end.
Most of the variations can be handled with dynamic text element in an index map without programming and you can export all the pages into a single PDF document.
If you want more variations than the basic dynamic pages you can program the layout.
Within a layout you can adjust all the major elements, change text and move spare elements stored off the page on to the visible printable area with a bit of python. You can have multiple data frames in one layout.
I can't see any issues with your workflow, but it is a bit sketchy. I suggest that you may need to just rebuild it and automate some parts a bit better and you surely would be able to avoid 35 MXDs. I have never had more that two. Maybe post a thumbnail of an example map/diagram?