I'm not sure why Adobe makes it so hard to install the flash player with a MSI. By going to adobe.com and clicking on the "Get Flash Player" link, it will direct you to a page that automatically will attempt to install Flash in IE. I needed a MSI because I needed to install Flash on a machine with restricted internet access. Fortunately, even though they don't advertise it, you can get a standalone installer for IE as well...
http://fpdownload.macromedia.com/get/flashplayer/current/licensing/win/install_flash_player_active_x.msi
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