When you do the recording, are you aiming to get (for each stop):
(a) just an audio file containing a 5-octave long-note chromatic scale with brief silences between notes, ready for you to cut up into individual notes? or
(b) 61 automatically-generated audio files containing single notes (with no extra work by you)?
Doing '(a)' shouldn't be too hard: you'd need software that would play the chromatic scales over MIDI and software that would record the audio; it could be a single program such as a sequencer that deals with both MIDI and audio, or it could be two separate programs. If you don't want to use a commercial sequencer (like Cubase), I expect you could find free software or low-cost shareware that would get you as far as making the recordings, and possibly free or low-cost software that would let you cut the individual notes out of the file.
As for doing '(b)', I wonder whether you could get the notes cut out automatically by one of those programs that do "beat slicing". I've never used one, but - as I understand it - they're able to examine an audio recording of a drum track and automatically find the starts and ends of each drum beat, and hence cut the drum track into pieces, each containing an individal drum hit. I wonder if you could use that kind of software to cut the individual notes out of the chromatic-scale recordings automatically - you'd still have to save the individual files manually.
Alternatively - "where there's a will there's a way" - I daresay that somewhere there is audio-manipulation software with a built-in programming language that would enable someone to write a program to do the whole job - just find the software and pay the programmer!
When you've got the 78 x 61 single-note sound-files, are you intending to loop them, or do you intend to make the samples long enough that you'll hardly ever reach the ends?