Hi lanternman,
To enter crop mode you have to press the magnify button on your 6d, (press it several times for different zooms, recording is always in 3x zoom and not what you see on the screen) but when magic zoom is enabled this doensn't work, so turn of magic zoom.
Zoom mode is always in 30 fps, even if your camera is set to PAL, so use FPS override function in magic lantern to use 25 fps or 24 fps in zoom mode.
For about 30 seconds recording I advise to use 1:2.39 aspect ratio and 1600 pixels wide resolution (giving you 1600 x 667 resolution).
This could still look good upscaled to 1920 x 800.
There is no way to record continuous in higher resolutions.
The problem is, that the internal memory buffer is filled up during recording, when the buffer is full, it needs about 5 seconds to empty it to the SD card.
That's the reason why the camera stops for about 5 seconds after recording.
There's no way to you can bypass the 5 seconds of emptying the buffer, unless you are a technician and can open your 6d and solder some more memory in to it
