You can get ChapterGrabber here. If that link doesn't work, goto this thread in the Doom9 forum.
VirtualDubMod actually comes with the Gordian Knot Rippack, but I had problems using Gordian Knot. Go here to grab the latest version of VirtualDubMod, unzip the file to the folder of your choice. Then, in the Gordian Knot options window, you can manually select the folder where you unzipped VDubMod.
For playing back files I recommend the free version of The Core Media Player (TCMP). It supports MKVs very well. Be careful when installing because this player is meant to play a wide variety of audio & video files; the installation program may change the file associations on your computer.
In the left column you choose the program chain that represents the movie. More than likely the program will select it automatically, otherwise you can select it manually yourself. In the middle column, there is a listing of audio and subtitle tracks available. Check off the tracks that you want to retain. Note that MKV files can handle multiple audio and subtitle tracks (I'm not sure if there's a limit at all), but using them takes up space in the final product reducing the quality of the video. You can also right click on the audio tracks to select the preset you want to use. There are six presets setup automatically. If you want to add more, simply goto audio preferences in the menu. I recommend Ogg 0.2 for movies, and Ogg 0.4 for music videos. Ogg offers superior quality at low bitrates meaning that video improves.
Just underneath these windows are a list of options. Simply click on the button to add or remove that step of the process. The steps are: