Just a few thoughts...

• MD is not a specially "different format", especially if you are comparing with with MP3.
  
• Given the lower sound quality of a typical portable MP3 solid state recorder, better to use MD and a plain simple analog connection to your sound card. Not as good a a digital connection but still better than typical portable MP3 recorders.
  
• The fact that MD isn't 'plug and play' in the sense described above is purely Sony's fault for delibartely crippling it that way. A stupid decision, but USB isn't the only way to connect things to a computer...
  
• Hard disk space is cheap! Store your audio in WAV files, especially if you are going through repeated rounds of editing and saving to disk. Repeated loading from MP3 to edit, then saving as MP3 will cause generation loss. Maybe when you have a final, fully tweaked and edited product you can save space by archiving as MP3 (use a reasonably high bit rate) or Ogg.
  
• Audacity is a free and very useable sound editor for Windows and other platforms It has a noise removal function, but like all noise removal functions that work the same way it doesn't work very well on people talking - it's best on continuous background noise like tape hiss (brilliant for that) or a humming aircon unit.
  
• In theory you can edit the waveform directly but with 2646000 samples per minute (doubled for stereo) you don't really want to do too much of that. It's a good technique for snipping out individual clicks and bangs, but even then an amplitude envelope tool or simple mark-and-delete may do the job quicker.
  

Anahata