Why not just use the self extracting properties of Windows Installer then?
This doesn't really address the 1603 error ("generic error" in installation) which seems related to ngen according to the logs. I've also found multiple ngen processes running after the installer. (I know that it just compiles assemblies to native code; I'm a .Net programmer.)
I managed to get one of the betas to install but I don't remember what I did to get it working. I tried upgrading it, didn't work. Tried to uninstall it, couldn't and had to use the Microsoft tool. I can't get it to install at all now.