newbie quesiotn about dvd5 to dvd9 guide

[astralwerks]

I recently tried my first attempt using the dvd5 to dvd9 guide, and ran into a few problems. After finishing the guide everything seemed to work correctly, however the move was in random order. It skipped to about 40 mins into the movie and all the chapter were messed up. I followed the guide exactly, however I did have to use dvd2avi 1.77 to get the dts stream. I use CCE 2.62, with maestro. What could be wrong here. After finishing the guide do I copy over all the authored files except the IFO and vts_0.vob, then using ifo udate point to the authored one and then the original that is now with the new files in one dir? Also I know this guide was to fit everything on one disc, but can I make the movie smaller, and include all the audio streams, instead of just using one?

Thanks for you help
Jeff