Jesse-
I would review the "Getting Started" section of the Flex Viewer Concepts page: http://help.arcgis.com/en/webapps/flexviewer/help/index.html#/Getting_started/01m300000021000000/ . My guess is that your IIS is not set up and/or you are placing the folders in the wrong place.
Also, keep in mind that the "/FlexViewers/" folder is just a sample location. You should be replacing it with where you are saving the Viewer folders on your server.
Myself as an example, I'm using the App Builder on my local machine to create the applications on the web server, 'gisdev'. I first map the C: drive of the web server on my local machine (\\gisdev\c$) and name it "G:". I am saving my apps at the web server's wwwroot folder level, so the path from my local machine to the web server is G:\inetpub\wwwroot\. Since I'm saving at this level, the URL to the web server's base folder (I'm using wwwroot) is simply http://gisdev/ .
EDIT: oh, and try using the newest application builder if you aren't: http://resources.arcgis.com/content/arcgis-flex-viewer-download
I hope this helps.