Bear in mind that checking the md5 hash (and the file size) would be appropriate and meaningful only for "binary mode" ftp transfers, as opposed to "text mode", where LF/CRLF conversion is applied during transfer. Text-mode transfers could systematically change file sizes (by adding or removing CR's next to LF's), depending on the particular server and client in a given transfer.

This is not much of an issue these days -- nearly all ftp transactions are done in binary mode by default now (and usually, ftp tends to be the tool of choice mainly for stuff that is intrinsically non-text). Still, if files are arriving with different sizes than you expect, this is a factor you should check on.