ASPECT RATIO
I agree with ReverendBeastly that we should keep this in 4:3. I downloaded an R2 DVD as a reference, and it had a number of shots where key parts of the image are cropped, as compared with the TV version. This is Waterworld, so I don't want shots like this where the water is cropped out:
TV Capture:

R2 DVD:

(NOTE: I don't have any screenshots of the R1 version, so I can't say that the TV cut is truly "open matte").
SOURCES
The sources will be my DV capture off of Bravo, ReverendBeastly and/or Llorang's full VHS TV captures, and the official VHS.
3:2 PULLDOWN
Being TV cuts, these sources need for each added scene to be IVTC'd separately from the film (correct me if I'm wrong here). I did a test of the hydro addict deleted scene and managed to get a smooth 24p, albeit with some strange chroma artifacts:

I used this in Avisynth:
DoubleWeave()
Pulldown(1,4)
The artifacts are barely noticable, but if it's a problem with my IVTC method, I'd rather get it right. If anyone knows of something I'm doing wrong, let me know. In the case of the VHS sources, if Jaiman Tuckuh is correct, it may not be possible to IVTC. Cross that bridge when we come to it?
NOISE
I've also tried out the Avisynth FFT3DFilter recommended to me by RidgeShark (he's using it for his Army of Darkness extended cut) and the initial trial is encouraging:
Bravo TV Original:

Bravo TV w/ denoise, levels:

LOGOS
Logos will have to stay. I don't like the blurry logo "removal" tools. Unless anyone knows of a filter which can truly remove the logos, I say just leave em and ignore em.
EDITING
Here's what I haven't gotten around to testing: Once the Different scenes are all individual 24p .avs files, I need to find some software to frameserve to Sony Vegas, where I'll cut everything together, color correct, and render out to DVD Architect.
I'm used to editing in Vegas, but have never followed this workflow before, so if anyone sees any potholes before me, feel free to point them out. Otherwise, wish me luck!