You can directly call .net 3.5 MSBuild from the command line by digging it from the frameworks folder in windows. I'm not sure if you could reassign Visual Studio to another copy. More importantly, if you did not find an error, a copy of MSBuild included in the .Net 4 structure should correctly build a project oriented to the 3.5 structure. This way you can jump through some unnecessary hoops in the first place.
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