I'd recommend using a ripping program that doesn't convert the video for you.
It'l take a little longer, take up more space and require a few more programs...but if you're aiming for quality then that's what you'll want to do.
the eadfag beta goes over what to do and the amvapp 3.0 beta has everything you'll need.
that said, if you insist on using your .mp4 files you'll have to use avisynth and virtualdubmod to convert your files to an editable format (usually using huffyuv or lagarith lossless codecs to put it into a .avi container)
refer to
this page for help on vdubmod and
this page for help on avisynth
When you do get around to making your script, download ffmpegsource() from
here and use that instead of directshowsource() in your script