* I enquired about this here but I couldn't quite put my problem into words and the post got messy. I'm not trying to double post to get an answer but rather to clarify. I'll be out all day and am generally not in a rush. *
I think the upgrade has created a permalinks problem that breaks more than just the index.php structure. The majority of posts on this forum in the past 24 hours have been about permalinks but I don't see a solution.
My structure is /%category%/%postname%/ and my site is here. Upgrading caused the following two things to happen...
I have a lot of internal links for navigation so using the default permalinks gives me a ton of 404's even with the permalinks migration plugin.
So, if I use /%category%/%postname%/ I get problems and if I use default I errors. I understand that something may have been wrong on my site before upgrade but it was the upgrade that brought about the problems. I am not alone in looking for a solution here.
If you point me in the right direction here I'll go though the forum and point everyone else with this problem to the answer!