I'll give you the benefit of the doubt and assume you've got perfectly good reasons for
1) still using FTP instead of SFTP
2) moving the service to a second box
Given that, you've pretty much got the right idea: build another box, put an OS on it, map the drives from the filer, and run the FTP service on the new system.
Though I must say that using IIS for your FTP needs seems....reckless. IIS isn't known for its security, and if you're moving your FTP service to another box in the name of security, this does not buy you anything. Especially since FTP sends passwords in plaintext (!!!!) and since the box has all your filer's data mapped to it anyway, anybody that pwns the new FTP box has essentially gained access to the filer anyway.
::shrug:: sorry if I'm not a lot of help; I run linux for all my server needs ;-)
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