Go to these sites and read the Guides presented there. I'm sure you will find something there to help you. http://home.comcast.net/~bbmayo/index.html http://www.dvdplusvideo.com/petesguide2.html
Also what are your system spec? My old computer 500MHz w/ 128 ram took about 2.5 to 3 hours. When I used Shrink on it - it also had high encoding times but did drop down. Shrink will start with a larger encoding time then it drops down.