I just started following this thread. I tried using my PC and sound recording software (Total Recorder, Sound Forge, etc) to move audio from my R900 reliably. What I found was that it was almost impossible to transfer hours of audio without introducing occasional skips/hiccups. Moreover, I needed to use my conputer for other tasks (email, web browsing, work).
After some experimentation, I found an excellent solution in the Nomad Jukebox 3. It can record up to ten straight hours of audio to lossless WAV or to MP3 format. Then you can upload the digital file to a PC in minutes. No skips or hiccups or extraneous noises in the re-recordings. The NJB3 even has an optical input for those with MD optical outputs.
For those who want a good, reliable PC method, a possible solution is the XP Media Center PC. The best of these PCs have a video tuner card which outputs a hardware encoded MPEG2 stream to the file system. Very little CPU power is used. These systems are designed to record TV shows in excellent quality without hiccups or skips even during use. A user could plug an MD line-out to the audio line-in of the tuner card and record reliably. On an HP M470 PC, this recording process uses less than 2 percent of the CPU. I can browse, email, and even do LAME conversions without affecting the recording transfer. I used to run an ATI All-In-Wonder tuner card on another PC and I could not even touch the PC without causing dropped frames. Not so with the XP MCE PC.