These artifacts all over the image are caused by different parity of timer A (compared to Canon value).
From the DNG, I can now do the math. Number of bad columns: 52 in the "good" image, 60 in the "bad" image. Difference of 8. Timer difference: 2 units. One unit of timer A reads out 4 pixels, so it adds up. The "good image" is off by 13 units, the "bad" one is off by 15 units.
The screenshot shows the last 50 columns, and all of them were bad, so I could not do the math from there.
0x21c + 13 = 0x21a + 15 = 553 units. Adding 1 since hardware register is written with timer-1.
Therefore, the minimum timer A value in 1080p is
554 (when doing the math for frame rate) or 553 in the hardware register. Canon default is 0x23b (hardware register) or 572 (when doing the math).
That means, in 1080p24 and 30, we can reduce timer A by
no more than 18 units (starting from default value of 572). In 25p, default value will be 600, so you'll be able to reduce it by 46 units.
This value (554) will give the lowest rolling shutter and the highest resolution at any given frame rate. Why not just using this? When aiming for a certain frame rate, timers can be set to integer values, so it may not be possible to get the requested frame rate with 3 decimal places. For example, 23.976 => timer B would be 1807 => 23.974 (closest approximation). For 25p => timer B would be 1733 => 24.998 fps. Or, 1732 => 25.012 fps. For this reason, we should try slightly higher timer A values that may result in frame rates closer to what we expect, but these higher timer A values will require lower values for timer B (which might limit the vertical resolution).
If you'll ever want to reduce horizontal resolution in 1080p (e.g. to get higher frame rates or smaller rolling shutter), you may reduce timer A even more. For example, if you are OK with 1872 pixels, you may use A = 552 (2 units = 8 pixels). If you want higher resolutions, you will need to add 2 units for every 8 pixels; however, on 5D2, you won't be able to increase active area beyond 1880 in 1080p; there are not enough pixels on the sensor. You can still request higher resolutions and get a "4K" frame good for April 1st announcements, if you want

Now it's your turn to do the same with x5.