Hi Cord ,
Which menu links is that? It could be as simple as going into the wordpress menu manager and re-building your menu. That is under Appearance >Menus.
The menu is the custom main menu I created under Appearance >Menus. I’m using it in the Incarantion Main Menu location. I tried deleting the menu and recreating it. Also, the blog links in the sidebar are not working, “The requested URL /uncategorized/post-5/ was not found on this server.”. Hope this helps.
Can we take a look at the site live? If its a permalink issue in general, there isn’t a lot we can do about it but maybe we can spot something by seeing the site live and inspecting the menu links a bit.
Absolutely, the site is temporarily hosted at http://cordvarty.dyndns.org/. So the “Roots” page, under “About Us”, is “http://cordvarty.dyndns.org/?page_id=46” and after permalinks is enabled, it is “http://cordvarty.dyndns.org/roots/”. Once permalinks is enabled and you use the old url, it forwards you to the new one but the page still doesn’t load.
I would suggest trying the permalink troubleshooting tips from the codex: http://codex.wordpress.org/Using_Permalinks#Fixing_Permalink_Problems
If you happen to be on a windows server, there are more complicated issues but the above link addresses them.
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