Thanks everyone for the contributions.
Sir Loyne - I tried converting an epub to kepub, via Calibre, and you were right it makes a huge difference (the converted e-book is far more responsive to line spacing, margins etc.). I just don't think the Kobo Aura One handles epubs very well. I decided to do a factory re-set and remove all the epub patches and just keep KOReader on the device. I only use KO Reader for PDF files.
I installed the Kobo Touch Extended plugin and the kepub batch convert plugin. It might be a nuisance to convert every epub to a kepub but that is what I do when converting an epub to a mobi for the Paperwhite. The only difference is that I can do it online and send it direct to my Kindle, via my email. However, the excellent hardware and larger screen with the Kobo makes it worth it.
ZodWallop - I tried the plugin with one epub conversion and it works. I can now alter all the margins (top, bottom, left and right). Of course, this is just one epub, so not too sure how it works out with others. I only wish Kobo will let us remove the header and keep the footer only. The full screen patch allows you to remove both or keep them. Anyway, I don't mind too much, due to the larger screen. I can understand how annoying it would be with a six inch Kobo.
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