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Is it possible to have the empeg appeare as a drive letter in windows so I can just move the files that way?

No.

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I tried the FTP function, but that's not for moving music files, is it?

Correct.

The problems you're experiencing indicate something else is going wrong. Perhaps something wrong with the hard disk, or with the network connection. See if you can upload with USB (after reading this).

Also, are you absolutely sure you used the builder image properly? For instance, if there was already data on the disk, it would say "disk appears to be already built" and require you to press Enter on the serial port before it formats the disk. And if there are two disks, did you run builder twice, once with each disk in the primary slot?
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Tony Fabris