Hello Bradley,
About use KDS on Windows , do not need care about this "KDS v3.0.0 Source Files Package.zip" .
And after you install KDS 3.0, i recommend you install KSDK1.3 , for some chips driver are supported on the KDSK1.3,
you can download it here :
Software Development Kit for Kinetis MCUs|Freescale
and about how to install it in KDS, please refer to the DOC of "KDS_Users_Guide.pdf"(under the installation directory of KDS : Freescale\KDS_3.0.0\doc)

Hope it helps
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Have a great day
Alice