[troubleshooting] Problem upgrading 2.3 to 2.5 / lost access to discussions and dashboard

I just upgraded from 2.3 to 2.5.1 and I am, well, stuck.

Here is what I have done:

• Overwrote all files with new files, then made sure I kept my old .htaccess and /conf/config.php
• I noticed that doing this overwrite modified my files and folder permissions, so I made sure that all my folders are chmod at 0755 and all files are at 0644
• I deleted /applications/vanilla/controllers/class.settingscontroller.php as well as emptied /cache
• Last: I noticed that the new config-defaults.php is bigger than my old config.php, so I created a new config.php with that new code.

The end result is that:
1) I do not have access to /upgrade/utility - Should I?
2) My forum home page displays correctly, but I cannot open any discussions and have lost access to the admin dashboard.
3) It doesn't matter whether I use my old config.php or the new one with the updated code from config-defaults.php. The end result - described in 2) above - is the same.

Questions:
A) What to do?
What are the correct folders and files permissions for vanilla 2.5.1 ?

Thank you!