Got an idea for mv1080. After enabling the 3x3 preset in crop_rec, run this from don't click me, while in LiveView 1080p:
EngDrvOut(0xC0F06804, 0x4a601d4);
That should change the raw resolution on the fly. This particular register is changed only when switching video modes, so the above should work. I've tested it on 5D3 with magic value 0x528011B starting from 720p 3x3 overridden to 30 fps. It almost worked (with corrupted frames).
Also make sure you have the generic PowerSave stuff enabled in crop_rec on the 3x3 preset. According to your latest log, it might be important. oops, that won't work; PowerSave registers are also set once when switching video modes; still, if you can get valid image with black bars at the bottom, that's a good sign.
Solved the corrupted frames by changing the HEAD timers. That should be done from a crop_rec preset, but first step is to get an image with the right dimensions; expecting only the top half to look fine at this stage.