Sorry that I haven't put up a file yet, I have few other things that need to be addressed immediately (i.e. my dissertation).
Yes, the percentage is tricky (since it isn't exactly a true percentage). Personally, I only use this script on files which do not crop using Heiko Oberdiek's "pdfcrop" (found or available on most Linux systems via the command "pdfcrop"). These tend to be papers from JSTOR, hence the skip first page option.
Thank you for trying it though, I will try my best to address the "left-crop" issue as soon as I have time.