First off; thanks for this awesome package! I've managed to get this far without having to post here.. :)
I've done the word-of-mouth thing with a couple of friends (webdesigners). :)

I've just upgraded to 5.4.1 through the dashboard and all seems to work okay except for two things..

I'm using the default yoghurt theme with a couple of changes. I'd changed the appearance of the main links in the header (next to the logo) to match the rest of the site, but after the update it's grey.. I've tried uploading the main.css and cleared the cache and all that, but the looks still remain grey... Any ideas on that part?

The second part is that my footer has changed to 'original'. I took out the login link to make it a little safer, but now it's back again. I did the same thing with uploading my own footer.php to the right place but it makes no change back to how I want it.. Any help?

Thanks for any help that you can give..!
-G-