Hi Fred,
I'm the guy who did the first batch of transcoding for you back in October, so I know what you're talking about and I already have semi-automatic scripts to do this. Are you interested in building a more general solution for this problem? I could develop this for you but I don't have too much capacity right now, I could deliver it between one and two months. There are some hidden complexities dealing with errors and rate-limiting (there's a limit on the number of jobs in the queue, the speed in which you submit jobs to the transcoder), etc.
Best Regards,