Sorry i haven't replied sooner but i've only just come across this thread as i have been staying away from the PC recently as much as possible.
What tools and methods are you using to create this as you haven't given any information? I noticed you mentioned that the program you used to rip the DVD couldn't do 5.1. Any DVD ripper worth using can rip the AC3 5.1 audio track without problems so i would ditch that program as soon as you can. Are you re-encoding the video too when ripping? If so what codec are you using and are you removing the 2:3 pulldown on the DVD? Another thing you haven't mentioned is your method of upscaling the DVD to your HD format
The main problem i see is the huge jump in quality between the 1080p source and an upscaled DVD. Even using the uncompressed source files i created for the reconstruction DVD it was too much of a jump for me between quality differences and that was at 720p, so it would be even more at 1080p (i am using 1080p because that is the res your screenshots are). And you are using a re-compressed 480p source that has already lost some detail. I was working @ 1024x576 and then scaled down for the DVD so there is some quality in resolution lost already. I wouldn't even be able to make these shots available because the uncompressed files are HUGE so uploading them would be a problem especially with my limited bandwidth. For example that wampa cave shot is just under 1GB.
Here are some screenshots that are upscaled to 1080p from my original files and i added links to the screengrabs you posted too so if each one is opened in a new window/tab you can easily switch between them and clearly see what i mean
Your Wampa cave
Wampa cave upscaled from original source file
Your removed window
Removed window upscaled from original source file
Your apartment matte
Apartment matte from original source file upscaled
As you can see the quality difference is very noticeable. This isn't anything against what you are doing but a result in having to use lower res/ compressed source.
Another thing i noticed is there is a colour difference between the original colour in the DVD and the files you posted, especially in the wampa cave. Is this due to the program you are using or have you altered the colour in any way?
What SE scenes are you keeping in because you haven't mentioned that also.
Please don't think i am knocking what you are doing in any way at all, because i'm not.