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This whole operation would be much easier if you could do it from the ftp server itself. Do you have sysadmin rights on the ftp server?
Can you 'put' the files from there instead of 'get' the files?...

One way to do this.
# Assume the filenames live in a file called "infile"

echo "USER username password
cd /remote/path/to/files
`for f in cat infile; do
echo get $f
echo delete $f
...