Uninstalling the .NET packages will only force them to be reinstalled by Win8 itself, and you can't use the individual installers like in Win7. It was interesting that .NET 3.5 wasn't listed in the active packages via add/remove AFTER CoD/Steam invoked the installer. So I done a force install of the packages and I also used the .NET repair tool for Win8 but still nothing.
Without the source code to everything its near impossible to debug this.
The manifest file you're reading just describes the assembies being used. Each manifest will be different depending on how you code your app. But it's not actual running code, it's meant for the CLR.
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