I want to write a custom action which will execute above all other custom actions and execute in system context. If I use "immediate execution" then it executes in logged in users context and if I use "deferred execution in system context" then this custom action executes after other custom actions. What should I do to handle this kind of scenario?
Only deferred actions can be executed in system context. It is executed at its scheduled sequence between other deferred actions. If this action must be the first action run, you would need a bootstrapper which will elevate permissions and the start your installation.
Note also: Deferred actions have very limited access to the properties of the install.