I’ve found the issue… for some reason virtualdub is outputting all screwy. My resulting AVI files are incorrectly set as DV NTSC pixel aspect ratio (around .9) with a 23.98 frame rate. My computer kept crashing so I was having to render in small chunks, so when I imported to Premiere I created nested sequences for each side. Those also ended up 23.98… but when I went to interpret footage it says 23.976… ugh.

Pretty much, my workprint is a good representation of how I want things to look and sound, but I’m having to start from scratch to deal with the issue.
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I’ll continue to work on this in my spare time, but it’s been delayed for a bit. My children’s mother attempted suicide on Monday and I am suddenly a full time single parent as opposed to 1/2 time.
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On a happier note, I have some leads on acquiring high quality captures of AotC and RotS on Letterbox VHS. With those as well, I will probably aim to release:
2 GB H.264/AAC MP4 files for each film.
BD-5 H.264/PCM for each film

A single BD-25 with all six films. I’ll render a menu in DVD Architect with multiple Playback Options - Play All by Episode Number, Play All by Release Date, Play All Machete Order, or Select Individual Film.

I’ll replace the m2ts files in the resulting folders with lossless h.264/PCM and run through BD Rebuilder set for BD-25 at max quality settings for h.264 and 640kbps Stereo AC3.