Note that I use a scanner with document feeder, allowing to scan multiple pages automatically.
1) Set skanlite to save in tiff format.
2) Join your multiple files, 1 per scanned page, produced by skanlite in one big file with tiffcp:
~$ tiffcp Image-0001.tiff Image-0002.tiff Image-0003.tiff all.tiff
This will produce the file: all.tiff.
3) Convert into a PDF file:
~$ tiff2pdf all.tiff > all.pdf
This will produce the file: all.pdf
At this point, I have my scanned pages in a PDF but the pages are in legal format. The scanned pages were letter format but skanlite produced pages in legal format anyway.
4) Crop the PDF so it will contain letter format pages:
~$ pdfcrop --papersize letter --margins "0 0 0 -175" all.pdf
This will produce a PDF file with letter size pages, removing the blank space coming from letter size pages being copied into legal size pages by skanlite.
This works for me, play with the "-175" value if you need to adjust, raising or lowering the value as needed. The tiffcp, tiff2pdf and tiff2pdf command-line utilities are available in Slackware64 14 where this was tested. They should be easy to install on your system if you do not already have them installed.