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What output profile are you using in calibre? As you are creating correctly sized images for your cover use "Tablet" or something that doesn't resize the covers. With that, you should be able to cut back to just the conversion in calibre.
Once the epub is on the device, what does the first page look like? This is what will be used as the cover. If your reading settings have margins, then they will be used on the first page and the covers.
If the above doesn't work, I am curious about what is happening. Can you post an epub after the conversion for me to look at? If you can create one with just the cover page, that should bypass any copyright considerations.
Having said that, have you looked at the configuration for the Kobo Touch driver in calibre? You need to set two options: "Upload covers for books" and "Always upload covers". With these options, the driver generates the covers at the appropriate sizes and copies them to the device. It uses the cover in the library to do this. The covers are stretched to the sizes, but if you have 600*800 covers already, they will be OK.
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