I think some of the issues with navigation right now are simply going to resolve themselves thru using the site. But one thing that would help immensely is having different shades in the background for alternating threads (and within a thread, alternating posts).
I did find the setting sections and tinkered around with that. For example choosing 'slate' may be my preferred setting. But once I set it to slate and open up a thread, the first post should be that dark grey, the second post, light grey, third post back to dark etc.
Interestingly enough, the settings section does this to an extent by making the categories you have to choose from a very pale grey on the white background.
Its a very nice contrast or border that makes it quick and easy for the eye to delineate between posts without any thought or searching.