TiffPrep allows you to split your multi-page Tiff files into separate documents (multi-page or single-page) and allows you to rotate specific pages and then output to TIFFs or PDFs. This can be much easier than scanning a stack of documents separately.  We built this for customers when we couldn't find another tool to do this for them.  It's still the only one that lets you decide where to split your documents.

TiffPrep 1.4