Hi. I've been encountering the same problems.
1) Uncategorised category doesn't get created properly during the upgrade. If I go into the categories section of the control panel and edit the Uncategorised category, change the status to publish and save the entry, then it works properly. By the way, I encounter a similar problem with any new category that I create from the control panel. The same work around works for the new categories that I create.
2) Front end SQL error after the upgrade when going into jDownloads. Being as I have a test instance on my server, I was able to set the debug on and get the debug information. By the way, I did the set the 'Display Category list box in Header' to No workaround suggested earlier in the discussion and it got rid of the front end error.