hmmm... A couple of things come to mind. First are the posts listed in the sidebar posted in the blog visible at index.php, or maybe does the blog on index.php aggregate posts from the blog the posts are actually in? What happens when you change your skin to either the stock version of 'custom' or 'evopress'? One would expect all usual and customary stuff to come right back, unless you've modified core files to reach your goal.

Assuming selecting 'original custom' restores normal stock stuff, then I would suggest you begin your edits again only move a bit slower. It sort of looks like you hacked out the entire posts loop is the thing.