Multitask, thanks for your answers.
Regarding 1, if you've got 800GB of music, surely you've exceeded the 1500 folder / 15,000 file limit? That may explain why you've never seen 100%. I've noticed that the indexing appears to proceed in alphabetical order by song, so you may want to try looking for a song you know is on your drive and begins with a W/X/Y/Z letter and see if its accessible.
Regarding 2, I wish some other folks could weigh in with their observations. Surely someone out there has a 20GB-60GB music folder on a USB or SD??
Regarding 3, switching between iPod, radi