Have you tried an Oak Technologies "Atapi" boot disk? Boots into dos with CD supported allowing you to run setup? Try looking on majorgeeks.com or bootdisk.com
My guess is yes, then it won't run setup from dos. (Sorry, but it's been a couple of years since I did this!).
I seem to remember I used to use an upgrade Win2K disc and that used to load Win2K quiet happily.
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