1. I fixed the weird pulldown issues by manually IVTCing and using DGIndex to fix the field-order transition errors. I verified that it's fixed by running an IsCombedTIVTC analysis pass and examining the (minimal) output.

2. I found the 3 missing frames. They were the last 3 frames before the shot where Neo enters the room to see The Oracle. I simply froze the last frame in that shot 3 times to keep it synchronized with the DVD. I will verify that the two are truly in-sync with my DumpShotChanges Avisynth function soon.

3. I fixed the horizontal aliasing by doing an nnedi2_rpow2(2, qual=3) followed by a ResampleHQ for downscaling to the final resolution (see #4).

4. You_Too helped me determine the correct geometry by manually registering some frames on top of the DVD (at 853x480, of course). We determined that the correct DAR should be ~1.75:1. The final "active" resolution will therefore be 1262x720.

5. I intend to mask the macroblocking by using a 120-frame Kodak 2383 35mm grain plate generated by poita. He says that this is likely to be the same film stock used for the release prints.

6. I intend to replace the end credits with upscaled NTSC DVD footage. Yes, it's letterboxed, but what more can I do?