Maybe this will help. Sounds like you need to run command lines after the install is complete.
1) create a batch file with your commands, ie. the installUtil and NET Start commands - save as install.bat or any name you want. You might want to add "pause" (without quotes) to the end of your batch file to verify it has run.
2) create a visual basic script file (install.vbs) with the following code:
Set WshShell = CreateObject("WScript.Shell")
strPath = "C:\your path here\install.bat"
WshShell.Run("""" & strpath & """")
Set WshShell = Nothing
3) Right-click the setup project, click View -> Custom Actions
Right-click Commit, select Add
Double-click Application Folder
Click Add File
Browse to install.vbs and add it
4) Right-click the setup project, click Add -> File
Browse and add the batch file (install.bat)
When your setup/deployment exe is done it will call install.vbs which will run install.bat which will run your command lines.
Hope this does it.