We build all our stuff in "kits" as you describe. We don't have much trouble running short on parts at the end although most of our equip. is new which helps a lot. We also have feeders that can run in reverse on set-up stations and we reload parts during feeder loading if it's larger package size. A couple tricks we use are adhesive "lead extenders" and cutting the front end of the tape to a shape that runs through the feeders more reliably (cut the sharp corners off). If your feeders are not so reliable, you'll need to figure out the scrap rate for various package sizes and have them issue the kits with overages for you.
(http://www.smtnet.com/Forums/Index.cfm?CFApp=1&Message_ID=66294)