My work-flow is,
We have Minolta (I think) photo-copier that has scanning option too. It scans as fast as you photo copy a sheet of paper. So I scan the whole book as a pdf file at 600dpi resolution. It usually creates a huge file. I take that pdf to Acrobat and export it as 600 dpi tiff files. Each page is converted to single tiff file so I usually end up with few hundred tiff files. Store all these tiff files in folder. Import this folder in
ScanTailor and thats about it. Scan Tailor will take care of all the things you mentioned. Once whole processing is done, export processed images as 600dpi tiffs. Assemble into a pdf file.
So far this works fine but I usually end up with quite big pdf file. I understand that it doesn't have to be 600dpi but I just don't know whats the best. Should I go with tiff images or png would also work? I don't know. I have tried running OCR on these huge pdfs and downsample it to 150dpi but not all pdf turn out to be good so I don't know if there is any yardstick for it.
I have not looked into pdf file structure and how best it can be manipulated so that the quality of images in pdf is good enough, at very small file size. I am searching for these options and I may modify my workflow accordingly.