So I finally found some applications to change .mkv files to .m4v/.mp4 without taking hours to convert the file itself. The two best ones that I have found are Subler and MKVTools. One problem, though. I can add videos (720p) remuxed from .mkv to .m4v using Subler to iTunes but they won't sync to my iPhone 4. I'm thinking it's because the audio codec in the files is AC3 and iTunes needs AAC. I can't figure out how to do that using Subler. Everything works fine with MKVTools, but it takes at least ten to fifteen minutes longer, which is inconvenient for remuxing several TV show episodes. Any help would be appreciated.