Sorry for the late reply

EDIT: when I turn off mlv_rec it does not show an error but this way I can not use RAW mode. What is the sollution to this?
For raw recording you either use mlv_rec or mlv_lite, you can't use them both.
mlv_lite supports lossless compression, so use of mlv_lite is advised. So best to not enable mlv_rec module.
1) I tried to use the 1x3 preset "5496x1960". When reviewing it at home the video looks not sharp and kinda blurry. Any ideas why this happens?
The 1x3 presets are not supersharp, the reason, the data is not saved as 5496x1960 but as 1832x1960 resolution. The sensor does horizontal pixelbinning, 3 pixels become one.
So the sensor does really readout 5496x1960 in pixels, but passes this data on as (5496/3 pixelbinning)= 1832 horizontal pixels x 1960 vertical pixels.
In post, for example in MLV_App, these 1832 horizontal pixels are stretched to the original 5496 pixels for normal aspect ratio.
So 1x3 is not as sharp as you would expect from the resulting resolution, because some trickery is used that is available at hardware level of the Canon camera.
2) When I shoot in 1x1 with 5x crop i can get a resolution of 2560x1440. I need to upscale this but which is the best way to do this?
In my experience the free software, DaVinci Resolve from Blackmagic does a really good job for upscaling video. (for free, download the normal version, the studio version is the paid one)
It's not that intuitive to use, but there are a lot of tutorials availabe on youtube.
https://www.blackmagicdesign.com/products/davinciresolve/ 3) When I am trying to shoot in 1x3 I can choose the preset "4896x2160" but then there are only magenta, pink lines across the Live View. Any ideas why?
Unfortunately, this is normal
I couldn't get normal liveview to work in this mode, you could however use ML preview to see what the recording will be like.
You can choose different preview options in the 'RAW video' submenu. It's on the MOVIE tab of Magic lantern menu, highlight the 'RAW video' option and press Q button on camera.
Now the 4th option from above should show Preview, here you can set the option from 'real-time' to 'framing', whith the option framing selected, you should see a low resolution preview of your liveview (it's a little slow in FPS).
Another option, you could switch to 'framing' by doing a half press on the shutter button, while doing half press, you should see a preview.
I like this option, I use the half press to check the framing, and press record button, you can even do half press of the shutter button while filming, to check the framing.