Windows .exe/.msi releases

It would be nice to have a more regular, .exe releases for windows that also includes the source code, so no need to download it from github on first startup.
- What liblary should we use? PyInstaller, py2exe, etc.
- Single executable (unpacked to temp directory on startup) or normal, 6-7 file distribution?
- Signing?
- Automatization?
- Source code packed into .exe or separately in .zip/directory?
- What about updates?
- Plugins?
- Is it possible to submit it to Windows Store?
- Alternative .msi or .exe installer with autostart option?
- Where to store data/config file/third-party plugins?