Thanks to Roger Maddy, I now have a successful workflow for creating 3DS stereo movies. My process is outlined below. It's a little convoluted because I am on a Mac running Windows via Parallel. (There is no "Mac only" solution to this.) The process outlined assumes you have/can create two separate files for each eye. (As I am working with my own content, this was easy, but it's also not so bad if you want to take clips off of a 3D Blu-Ray.) I hope this might help others.
Apps you need:
Stereo Movie Maker -
stereo.jpn.org/eng/stvmkr/
AVIdemux -
fixounet.free.fr/avidemux/
KLite CODEC Pack -
www.codecguide.com/download_kl.htm
DVD Fab - If you want to rip stereo movies from BD.
How To:
1. Use AfterEffects (or something similar) to scale each eye using chart below:
400x240 (1:1 Recommended)
1920x1080 = 20.8% of Original
1280x720 = 31.25%
720x480 = 83%
480x240 (Convergence Adjustable. Not recommended.)
1920x1080 = 25% of Original
1280x720 = 37.5%
720x480 = 55.6%
NOTE: 3D-BD Clips sourced via DVDFab may need an audio offset of up to 29 frames. if offsetting audio, export a new WAV file that is the same length as the source video and merge in AFX.
2. Export each eye into separate PJPEG QuickTime movies (other CODEC acceptable as well). The Left Eye should include audio, and the Right Eye shouldn’t. NOTE: A complete windows workflow can create AVI's at this step out of AFX, but it cannot create the MP3 audio that SMM seems to prefer. (Roger's tip.)
3. Using AVIDemux (Mac or Win), process exported QT movies into AVI’s. For Left Eye, set Video Output to “Copy” and Audio Output to MP3 (lame) at highest settings. For Right Eye, set Video Output to “Copy.
Using any other audio format than MP3(lame) seems to cause SMM to crash consistently.
4. Transfer resulting AVI’s to Windows.
5. In Windows, open each eye in Stereo Movie Maker. (Note: If you get an error when opening, be sure to install the KLite Mega CODEC pack.)
6. Then choose, Save as 3D-AVI.
7. In the pop-up window, choose the setting on the lower right that matches your frame size and rate (20, 24, 30), set quality to nothing higher than 75, and uncheck “Preview while encoding box.”
8. Rename exported 3D-AV in the format LLL_####.AVI. The number sequence cannot match any other image or movies number even if the letters are different.
6. Copy to DCIM folder on 3DS MicroSD card.