I think I figured out my Doctor Who DVD problem. In decoding I kept getting a 29.97fps file. I kept trying to follow Cap's guides and get it fixed, but it's not exactly a situation he describes, more like the opposite (he describes how to make a PAL DVD into NTSC but not how to reverse the process). So I put it away for a while. I just happened to decide to try again and cobbled together an AviSynth script that would convert from 29.97 to 23.976 and then speedup to 25fps and alter audio and everything, and after running it, ta-da! Corrupt file. I botched something, no idea what. So I searched some more. Someone provided a partial solution with a script for someone with a different but similar enough situation. I was able to remove the unnecessary parts and use the rest and decided to just try to run it even though I don't really understand what it's doing, apparently it's for reversing a 6:5 pulldown which sounded like what the dvd might be, considering the pitch and length seemed correct even at 29.97.
Anyway, it SEEMS to have worked, pulling the resulting AVI into my editor the video plays smooth like butter at 25fps and going frame by frame I'm not seeing any weird jumps or blends or leftover interlacing. Posting this for people who may search for an answer for the same problem. If it turns out this isn't the answer then I'll edit this post and remove the bad info. Already I'm noticing the audio isn't lining up exactly, maybe there is a time difference to account for.
The avisynth script I used (with the file path obscured, replace the path in quotes with the path to your d2v file generated by dgindex following Cap's guide in his FAQ) to turn a US NTSC Doctor Who ripped disc file back to its original 25fps state and into editable color space :
Mpeg2Source("D:\Disc Copy\VideoFile.d2v")
AssumeTFF()
separatefields()
tfm(display=false, mode=1)
tdecimate(display=false,mode=1,cycleR=2,cycle=12)
weave()
AssumeFPS(25)
ConverttoRGB()