I think MPEGStreamClip will work for this. As long as the .m2v and .ac3 tracks all have the exact same name besides the extension, then you should be able to use MSC to batch open all of the files and export to mpeg program stream (.mpg). Only downside is that on a PC, this could take forever (I recently had to do a similar conversion). On a mac, I don't know how long it would take.
Right, and MSC should do this. If you import a .m2v into MSC and there is a .m1a or .ac3 with the exact same file name in the exact same directory, then it should automatically recognize the audio and mux it internally within the app. And then if you choose the export to mpeg option, you will have a fully muxed mpeg file.