UPDATE:
While looking over these episodes with @SpacemanDoug, we discovered that there are extended versions of nearly every episode in season 3. There is also an extended version of the series finale. However, the rest of the episodes (all of season 4 and all but the final episode of season 5) appear to have the same episode runtimes as the versions that were released on blu-ray. (I’ve edited my original post to reflect this.)
That being said, every episode I’ve checked from seasons 3, 4, & 5 has altered music on blu-ray (& streaming) compared to what originally aired.
I have started the process of restoring season 3. I’ve completed the first episode, and I have mixed feelings about the end result. I’ve tweaked the upscaling settings to achieve the closest possible look to the 1080p versions on blu-ray, and many of the shots look very good; a few shots definitely do not. (When upscaling low resolution footage, close-up shots tend to look great, medium shots are hit-or-miss and wide shots with people’s faces in them often get weirdly distorted.)
As a proof of concept, I can make the completed version of episode 301 available to whomever is interested.
If there is enough interest in the complete season and/or seasons 4 & 5 with the original music, I will continue to work on this project. (It will certainly take a lot of time, as the process is quite tedious.) If not, I’ll probably put it on the back burner or abandon it. The additional footage and extended scenes are interesting to have access to, but they’re clearly not necessary for the enjoyment of the show. In my opinion, having just done the one episode so far, most of the DirecTV exclusive content adds very little.
For those interested in what was changed for episode 301, I’ve included the list of changes below. (Note: In order to preserve the original music, I used the stereo TV audio for the entire episode, except where noted.)
List of changes:
00:00:30-00:00:35 - Extended shot
00:03:37-00:03:40 - Extended shot
00:03:46-00:04:58 - Extended shots, additional footage
00:08:36-00:10:39 - Extended scenes, credits adjustments (the beginning of this section is perhaps the best example of how bad certain shots look when upscaled)
00:13:03-00:13:08 - Extended shot
00:14:26-00:14:29 - Additional footage
00:17:37-00:17:41 - Extended shot
00:18:37-00:18:41 - Additional footage, extended shot
00:19:54-00:20:27 - Extended scene
00:25:52-00:26:02 - Used ADR audio from blu-ray, which was recorded to correct a continuity error in the original dialogue
00:28:04-00:28:44 - Additional scene
00:41:17-00:41:36 - Extended shot, re-ordered scene
00:41:36-00:43:29 - Extended scenes
00:44:19-00:46:21 - Extended scene