In recent times, upgrading ISPConfig in a production server seems not out of chaos!
I dont think so. There are several thousand successfull upgrades already to 3.0.4, also all my servers upgraded without a single problem by just running ispconfig_update.sh. Its sad to see that your upgrade failed and I will try to help you to find the problem, but you should be aware that you not only installed a ispconfig update, you also installed and compiled a lot of system software at the same time and the software versions and compile settings that you used to install the software had not been tested on centos with ispconfig. The tested setup is what you find in the perfect setup guide, if you use different software or software versions, you will have to check if they and the compile settings ypu used are compatible with ispconfig.
If you had this problem already with ISPConfig 126.96.36.199, then you should post which solution you used that time so I might be able to tell you what the reason for the problem is.