The Cakewalk sequencing software has a very powerful, but very poorly
documented, feature called "Fit Improvisation"  This can be used very
effectively for aligning a piano roll scan converted to MIDI.

The Fit Improvisation allows you to select the notes that should be at
the start of each measure throughout the piece.  After performing the
alignment, you can then quantize the start times and lengths of the
entire track to make everything line up to the nearest 8th, 16th or
whatever note length is appropriate for the piece.

This will then give a much nicer starting point for editing to put the
piece into standard human notation.

Regards,
Warren Trachtman