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With a complex process like you're describing, you can follow a couple of different paths. If the original project is automatically installed, you can have the reboots occur when needed and have the project exit undone until all steps are completed.
You then put at the beginning of the project logic that checks to see how far along in the process you've gotten and jump to the next step as needed.
You can also have the main project just call other projects that do the individual steps as needed. You'd need to use InitiateSystemShutdown, EndInstallerSession and ExitProc(Undone) and so on to control the process. Use EndInstallerSession to insure other queued projects do not start and ExitProc(Undone) to make sure NI wants to continue executing the master project.
If the master project is only executed from the Interactive Installer but you want it to run to completion after it has started, you can use RegModify to put the command
into the RunOnce key. NI will convert the variables to the actual values as it writes the command to the registry. (HKLM\Software\Microsoft\Windows\CurrentVersion\RunOnce) to have it continue execution following the reboot and subsequent login. Put the command in before each reboot is initiated so that it will pick up where it left off. You'd still need the logic within the project to make sure it knows what step is next required.