My way wich works Great in 99% of the time (some fonts somehow dont work with mobipocet creator i use abby finereader 9 wich takes way longer then mobipocketcreator but is just best with alot of pictures and stuff)
So my way is :
1.Bris : Crop that side Numbers
2.Mobipocket Creator : get a nice and clean Html File
3.Sigil : Ebook Editor. with Regular Expression and a bit Coding expierince you clean up ALOT of errors and get a almost perfect ebook in a few quick Steps. i list them at the bottom if your intrested in trying. Safe the Epub
4. Calibre Converting, 'Metadata Edititng, Transfering etc
Sigil Steps
1. open html
2. push F11 (Code view. dont leave it till the end)
3 push Ctrl+H
now check that the replace is set to REGULAR EXPRESSIONS. then just copy and paste the following commands and replace all
(<p class="( |sgc-\d){0,3}">(\s*|\S*){1,15}</p>)
replacewith
\1</a>
(<b>(\s*|\S*){1,10}</b></p>)
replacewith
\1</a>
([^(.|?|!|<|>|«|"|:|“)])</p>\s*<p>
replacewith
\1SPACE
dont write out the space here, do it
([^(.|?|!|<|>|«|"|:|“)])<br />\s
replacewith
\1LEERZEICHEN
<br />
replacewith
</p><p>
5. Switch back to book view with F9 and watch what youve done (&and save it ^^)