I found a solution to the too many mysqld processes. I just compiled mysql with none of the extra flags (just prefix) and it worked.
Code:
./configure --prefix=/opt/zimbra/mysql-standard-4.1.20-pc-linux-gnu-i686-glibc23
I now have a working CentOS 4.4 Zimbra build (4.0.4_GA_494)!
Does anyone know if there is a way to checkout the 4.0.4_GA_457 version from SVN? Are the updates put into the EDISON branch safe enough for production?