What he just said!

It's quicker to do it by hand from scratch than to waste time trying to put right the howlers that software will inevitably produce.

Some years ago I was involved in transcribing card books from fairground organs to MIDI... we adapted a key frame to send the output to a MIDI decoder, and 'recorded' the results using Cakewalk.

As the prime purpose was to obtain MIDI files to 'play back' via a floppy disk MIDI machine on a MIDI-enabled fair organ, the results were perfect... however, to look at as a musical score it was hopeless!

Unfortunately, any effort to quantize or otherwise make the results readable as a score rendered the MIDI as useless for 'playback' purposes, as it completely lost the 'swagger' typical of a fairground organ.

Good luck - you're going to need it!