Avisynth can help clean up footage. We can help you clean up your source, but we'll need a few screenshots to see what needs to be done.
dvdDecrypter should do the job just fine. Any dvd ripping program should do the job just as well though (as long as it doesn't force you to encode the rip with divx or xvid)
Dunno what's in the amvapp 2.1, but the newer amvapp 3.0
does list what it has. The only thing is that the amvapp tests will fail on Vista (but you can ignore the test failure, everything will work)
Zarx264gui 1.0 has some issues, an updated version can be found here