I would try the following:

1. Connect a cord from the Minidisk's earphone output to the computer's microphone jack.
2. Play the music.
3. Run some recording software such as CoolEdit2000.
4. Do some minor editing of the resulting music (e.g., remove blank space at the beginning and end, normalize the volume level).
5. Save the music (as wav or mp3).

Personally, if the original music was on 45s, I would play the 45 (instead of the Minidisk) when recording to CoolEdit. This is because you've copied the record once to go to Minidisk, and then again to go to the computer. That's a copy of a copy. The music on a MD is compressed in a Sony proprietary format, and that is not the same as a wav file. I believe you may lose some fidelity going from record to MD to computer instead of going from record directly to computer.