If I made a fake fasta with 10x the material of a book, randomly cut and spliced, and use this to align a Book, could tophat2 reconstruct the book? Or it only work with with ATCG letters?

Just a question that came out in my mind today.
You would need to re-encode the book as ACGT. For example, 1 ASCII character is 8 bits, corresponding to 4 nucleotides if you use the simplest possible encoding (rather than trying to pack into 7 or 6.5 bits, or whatever). Thus for an ASCII-formatted text file of the book, the encoded book would be 4x as long, but the mapping would work fine.

You MIGHT be able to map to the raw book using some protein aligners, as those allow more symbols.

As Istvan said, though, you'd need to use an assembler to reconstruct the book, not an aligner.