> Can HTTrack follow a HTTP-EQUIV="Refresh" command?
Only if you authorized the site using scan rules - example:
+ftp://ftp.foobar.com/*

> Can HTTrack download from an ftp server as well?
Yes - but it is advised to use more specialized softwares 
(httrack is not very good at downloading ftp files - this 
is only a supplemental feature for separate ftp files)