The Clara HD and the Shine 3 are the same piece of hardware.
I've used the Clara, but not the Shine. But given that you like to tinker and you like to sideload your books, I'd say go for Kobo. You can patch it and mess with it endlessly. Or leave it as it is.
Kobo is good with sideloading wiuth Calibre so you can set series information and collections.
On the other hand:
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...buying Tolino is easier and cheaper, too.
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I don't know what the price difference is or if it is worth the difference for the features Kobo has.