A couple of options for cropping PDF files, none of which is perfect for all needs, and all are awkward, to say the least.
1. Briss http://briss.sourceforge.net/
This is a gui that I believe to be portable (requires Java). It allows up to 2 crop boxes per page, and while it is not intuitive, right-clicking the boxes, will give you the sense of it. It was created to prepare PDF for eBook readers, so its limitations are assuming most crop boxes have that as a goal.
2. cpdf. CLI talked about at viewtopic.php?f=22&t=23606&hilit=cpdf#p99331
I use this for many other things, but if you measure the points, it can do almost any kind of cropping you want. Be prepared to create many pages that need to be put together.
3. K2pdfOpt meaning Kindle to PDF Optimizer, writes to registry at HKCU\Environment, which keeps the session settings. See discussion at viewtopic.php?f=20&t=21561&hilit=K2pdfopt
Does a credible job using default (tested on some published studies that go from single- to double-column with graphs, etc.). If you clean up the four or so settings in HKCU or may a YaP for it, this might be good to use. I recommend running
so the preview pane shows the crop boxes. There appear to be a lot of options to modify things, such as ignoring headers and footers, so I will want to play with this when I have time--go to the many help and customize pages here: https://willus.com/k2pdfopt/help/
I won't have time to play with these for a few weeks, but if any of them help, let everyone know how you made them sing.