I've never written a guide for AVStoDVD cholla. I don't think I've ever used the Join Source Titles function either.
When I import a dvd video, I almost always combine the vobs into one mpeg file before importation. I use Vob2Mpg for this normally. Some conversion programs will handle dvd-video without this step of course. When going to H264, Handbrake works with dvd-video with no issues.
Since I didn't have a PAL dvd to experiment with, I made one from an avi tv capture file I had. Converting the xvid avi to PAL elementary streams in AVStoDVD went without issues, but going from PAL to NTSC needed a few extra steps.
The first thing I did was use DGIndex to create a .d2v file of the PAL video stream. When starting with a PAL dvd you would use DGIndex to create a similar file, and demux the audio and video streams into separate files. Or you could use PGCDemux to get them into separate streams and then run the video through DGIndex to create the .d2v file.
Then in Preferences-->Video within AVStoDVD I removed the check mark from the box that says Keep Mpeg2 DVD Compliant Video. Click on OK to save this setting temporarily (or you can check the box to make it permanent, but I don't recommend that). I also made sure that the program was set to make an NTSC dvd.
Import the d2v file. If you have the corresponding audio in the same place, AVStoDVD should find it and bring up a pop-up box with it. Just close out the box. If this pop-up doesn't show, you'll need to right click on the d2v file in the main window of AVStoDVD and search for the audio to import it.
Once that is done, click on View/Edit Title Settings on the right side of the main window of AVStoDVD. Go to Video, remove the check mark in the box next to Auto Video Setup and put the Video Encoding Profile to HCenc 2 pass. Click OK.
Make sure you have output set to go where you want it, and make sure the pop up box that comes up says you are making an NTSC dvd video. Start the encode.
My result from this was an NTSC dvd-video that plays flawlessly on my computer. No jerkiness at all. I haven't burned to a disk and tried it on a standalone player yet, but that is the next step.
You'll notice that I didn't try to use DGPullDown. I let AVStoDVD handle that step in combination with HCenc. It seemed to work fine for me.