Help! Can't navigate to any post from home page!

[pakzaban]

I upgraded to WP 2.8 after I had set up my site (http://www.pakzaban.com/arts). I noticed that I could no longer select and edit the code after I had upgraded (the code was greyed out and not selectable). Otherwise everything was working fine. I rememberd that in the upgrade process, I had not upgraded the wp-contents folder and thought maybe this was causing the problem. I did the following things: 1) deleted the old plugins folder and replaced with a new plugins folder that only has Askimet in it, 2) and replaced the index.php file in the wp-content folder with a new index.php file. I did not touch the cache, themes, or uploads subdirectories in the wp-content folder. I am not sure what went wrong but I now have a major problem. I can load the home post, but can not navigate to any other post or page by clicking arrows, using drop menus or clicking on thumbnails. Please help!!!