Sorry but I fear noone can help you to put decently a PAL VCD source into a NTSC KVCD destination
Seriously, you can't obtain good result by enlarging the soruce resolution. So with a 352*288 (PAL) source, you have to do a 352*240 (NTSC) target.
As your original framerate is 25 and you want to go to 29.970; you should encode in MPEG2, at 23.976 and ask to tmgenc to use "3:2 pulldown while playback". This way your player will show the video at 29.970 and you won't have to deal with synch problems.
For the rest, ask precise question aboptu what you didn't understood in the guide. You will obtain more accurate answers.