Re-installing mysql from source means updating the mysqld binary,
this should not affect your current databases.
But, it is allways better to have a backup of your data before you update software.
To get the most out of mysql, read the manual!
It has tips about how to make it faster by re-compiling,
and by re-configuring.
Test the speed using the mysql "benchmark" functions, and see which method of compiling is faster for your server.