First the kernel boots, then it launches init, which uses the scripts in /etc/init.d/ to start up all of the system services. The final service to be started is lightdm which in turn starts xorg and then draws a login screen. man boot-scripts. The whole startup process, from boot loader to graphical login, is complicated, and understanding it all requires understanding how initrd works, how upstart works, how the individual init scripts work, how udev works, how xorg works, etc. Each subsystem has its own configuration scripts.
Do not expect to be able to learn it all overnight - it takes years to become an expert. I would suggest you start by reading the scripts in /etc/init.d/ and playing around with starting and stopping them. Most of the configuration files are, in general, found in /etc/ - if you look in that directory, you will find many files, each with its own purpose, each installed by some software. To find out which package a particular config file came from use dpkg eg. dpkg -S /etc/locale.alias will tell you that file came from the locales package. Some of these files have their own man pages (eg. locale.alias), for others you will have to read the package docs or search the web.