7zip Self Extracting Archive (SFX) and .Net Installer

I am trying to create a self-extracting archive for a Windows application that I wrote. My application uses the latest .Net 4.0, and I want to include the .Net installation in the SFX installer. However, if the computer needs to install the .Net infrastructure and reboot, it will not properly resume installing my application. I looked at other sfx messages on Stack sites, but none of them is a problem with the .Net installer as a prerequisite for the application.

My project creates 4 files: "App Installer.msi" "setup.exe" "WindowsInstaller-KB893803-v2-x86.exe" (in the folder "WindowsInstaller3_1") and "dotNetFx40_Client_x86_x64.exe" (in the folder "DotNetFX40Client"), all of which I consider standard.

I use 7zip to create SFX as follows:

First use 7zip to compress all files into one archive:

7z.exe a -r AppInstallFiles.7z *

Then I make a binary copy with the 7zS.sfx file (used to create a self-extracting installer), my configuration file and archive. The configuration file is as follows:

;!@Install@!UTF-8!
Title="MyApp Installer"
ExecuteFile="setup.exe"
;!@InstallEnd@!

And I copy them using the line:

copy /b 7zS.sfx + config.txt + AppInstallFiles.7z MyAppInstaller.exe

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