Here's what I did. It was a bit more involved than what everyone else was reporting. I tried doing a repair in the Control Panel, it ran for several hours and then failed. Perhaps my problems were that I installed VS2013 sp1 and then upgraded it to SP4 before I removed "Microsoft Visual Studio Asp.net MVC 5 Scaffolding."
I downloaded and installed Visual Studio Premium with Update 4 and then did a repair using that file, but the extension was still missing. I then found the AspNetWebFrameworksTools_VS12_ENU.msi in the en_visual_studio_premium_2013_with_update_4_x86_dvd_5935086.iso and did an uninstall and a reinstall, but the extension was still missing.
I extracted the packages\WPT\AspNetWebFrameworksTools_VS12_ENU.msi file from my .iso file using msiexec. In order to get the .msi file to extract successfully, I also had to place the *.cab files from \packages\WPT into the same folder I was extracting the .msi from. Once I'd extracted my msi file, I went into it's folder structure and found the Scaffolding stuff. It was in Dest\Microsoft ASP.NET\ASP.NET Web Stack 5\VS_12_COMMON7_IDE\Extensions\Microsoft\Web\Mvc\Scaffolding folder.
Once I had that, I still didn't have a .vsix file that I could install into Visual Studio. So what I did was create my own .vsix file. I did a little research on the web and created a file called [Content_Types].xml, it's literally called that. I renamed the file extension on several .vsix files that I had downloaded on my system to .zip and looked inside them to see what the contents of my [Content_Types].xml should look like, here's what I came up with:
<?xml version="1.0" encoding="utf-8"?>
<Types xmlns="http://schemas.openxmlformats.org/package/2006/content-types">
<Default Extension="dll" ContentType="application/octet-stream" />
<Default Extension="pkgdef" ContentType="text/plain" />
<Default Extension="vsixmanifest" ContentType="text/xml" />
<Default Extension="txt" ContentType="text/plain" />
</Types>
I then zipped up [Content_Types].xml, extension.vsixmanifest, and Microsoft.AspNet.Scaffolding.Mvc.5.0.dll to a zip file called Microsoft.AspNet.Scaffolding.Mvc.5.0.zip. I then renamed that .zip file to Microsoft.AspNet.Scaffolding.Mvc.5.0.vsix. I then was able to install the extension using this .vsix file that I created.