I'm enjoying watching your progress with this project and its looking excellent, but I'm curious as to why you're converting stereo files to 5.1? Most 5.1 systems have the option to up-mix stereo tracks on-the-fly during playback, so you may just be using up space unnecessarily on the disc.

Also, if you haven't tried it yet, eac3to is a command-line tool that can slow down those PAL tracks that have the 4% speedup (I've never tried it on pitch-corrected PAL tracks, so I don't know if it will do those without changing pitch), and it can output to AC3.