textchimp: I'm also using the same approach to "syncing" books. You may want to use the plugin's command chaining and its sync mechanism instead of simulating a usb connecting. Also, the busybox wget will not work with secure connections. So you may want to use curl instead.
I'm currently also using a simple php script with a simple interface to add URLs that I want the kobo to download. When I get some free time, I hope to do Dropbox syncing using their REST api.