Are you sure you want to convert them? The Kobo devices handle CBR/CBZ with not problems. From memory, they don't have a heading or footer. Plus you can zoom and rotate the images.
For the conversion, what do you have for the output device? I recommend using "Tablet" as that does the conversion without resizing the images. The Kobo devices will handle this.
As to the heading and footer, strictly you can't get rid of them. But, recent firmware have an hidden option. Adding "FullScreenReading=true" into the "FeatureSettings" section of the config file will add an extra option to the reading setting. This is "Show header and footer". Unchecking that will remove the heading and footing when reading epubs and kepubs.
If you edit the config file, make sure you use a text editor that understands Unix style line ends. Notepad does not. I usually use Notepad++.
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