First things first. Don’t blame WordPress 3.9 unless it is a clean install with no plugins and no custom theme. 3.9 is working beautifully on thousands of sites already with no problems.
If you are not running a high traffic site try disabling all plugins (or manually moving them from the /plugins directory). Also, enable the default Twenty Fourteen theme.
If you are running a high traffic site do whatever you can to get your site back up and then try to replicate the exact setup of theme plugins and 3.9 and work out where the conflict is by enabling the plugins one at a time.
All your problems are likely to be with some plugin or theme which has code that did not anticipate the changes made in 3.9 once you find out which plugin or theme it is contact the author and let them know that 3.9 breaks their code. Updates for well-maintained plugins and themes still can take a few days to roll out.