Simple. In between DVD2AVI and TMPGEnc, just use AVISynth.
Movie = mpeg2source("movie.d2v",CPU=4)
Extra1 = mpeg2source("extra1.d2v",CPU=4)
scene1 = trim(Movie,0,46564)
scene2 = trim(Movie,46565,0)
The above would take an extra scene insert it at frame 46565 and then contine with the original.
edit: Stupid me, the above would be video only, so you would either need to cut the audio seperatly or use AC3Source, decode to wav and use wavsource or try directshowsource with AC3Filter set to a stereo downmix.