Download and install ScanTailor if you don't already have it.
Scan images at 300 or 600 dpi grayscale and load them all into a new ScanTailor project. Run each of the processing steps and spot check for mistakes made by the automatic algorithms. At the output step, choose black & white and adjust the darkness slider so that it looks like the original (not too dark) but not light enough that detail is lost.
Run the output step, and look in your project folder for a new directory called "out". Use one of the ImageMagick commands below to convert all of the result images into a PDF. Suggested:
$ convert out/*.tif -compress Group4 output.pdf
The programs convert and mogrify are part of the ImageMagick suite and the program pdfimages is part of the Xpdf suite.
To extract all images from BestSongEver.pdf to bse-000.ppm, bse-001.ppm, bse-002.ppm, ... (color images end with ppm, b/w images end with pbm)
$ pdfimages BestSongEver.pdf bse
To convert every *.pbm image to TIFF using Group4 compression with a nominal resolution of 300pixels/inch
$ mogrify -format tiff -compress Group4 -density 300 *.pbm
To convert a series of TIFF images, in alphabetical order, into one PDF document
$ convert *.tiff MyNewDocument.pdf
To convert a series of TIFF images, applying group4 compression and a fixed DPI, into one PDF document
$ convert *.tiff -compress Group4 -density 300 MyNewDocument.pdf
To convert all TIFF images in-place to GRAYSCALE
$ mogrify -type Grayscale *.tiff
To convert all TIFF images in-place to BLACK and WHITE
$ mogrify -type Bilevel *.tiff
To convert a multi-page TIFF document into a multi-page PDF
$ tiff2pdf MyDocument.tiff -o MyDocument.pdf
To concatenate a series of TIFF images into a single multi-page TIFF
$ tiffcp page*.tiff MyNewDocument.tiff
To split a two-page scan original.tiff down the middle into page-0.tiff and page-1.tiff
$ convert original.tiff -crop 50%x100% page.tiff