I would try using expect. If for no other reason, just to add this amazing tool to your toolbox. Boiled down, it is a scripting language to automate programs that require user input. I.e. in this case ftp. You can write a *very* simple script that will upload just the files you want. I know someone that uses this to develop a whole website at home, and then just has expect scripts to tar everything up, upload it, untar, etc. etc.
I know this may be a bit heretical, but hey, the right tool for the right job, right? I'm sure we all believe that, no matter how much some of us wish to believe perl is always the right tool for the right job. ;)
Justin Eltoft
"If at all god's gaze upon us falls, its with a mischievous grin, look at him" -- Dave Matthews