Hi sparklemotion,
There's no reason why fonts and font-weights should be related to page margins so I'm a little confused what's going on. There are many ways to code the internals of an epub which could interfere with the Kobo's customisation options. Do you have time to try some experiments with an epub which has none of these problems? If so I can post one of my public domain epubs and we can experiment on that.
Geoff mentioned some of the ways the Kobos can be customised to control page margins. For standard epubs the kobo_extra.css is the simplest, least technical way to increase the top margin and to reduce any over-large bottom margin when it's caused by widows/orphans settings (or lack thereof) inside the epub. However, many (including me) still find the bottom margin too big. The best way to reduce it is using the Kobo Patcher program which Geoff has added all sorts of goodies to. Have you had time to read about this yet?
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