Me too - I think previously unread books should open on the cover... One more reason I'm happy that I didn't buy a Kindle
On your other issue, you might want to check out this link
http://amalthia.mediawood.net/tutorials/ebooks/toc.html
It's the Calibre help page about TOCs - the general recommendation seems to be that you shouldn't go to the effort of making a TOC - Just mark up the chapter headings and let Calibre take care of it. This is the way I do it - and it works great - mind you, I make epubs for my Sony.
Good luck with your editing
