I have an Amazon Echo paired with a Harmony Hub. I want to use Echo to tell Harmony to turn on my PC, and also to shut it off. I got the Flirc for that reason. However, I am limited with the things that Flirc can do.

I can only setup Flirc as Kodi/XBMC in Harmony. This is an issue because Kodi has limited commands. Ideally I want to be able to run command "CRTL" and "F6". I was thinking I needed to setup Flirc as a keyboard. However, Flirc does not setup correctly as Windows MCE Keyboard.

I have searched everywhere, and have yet to find one person with my similar situation. Can anyone help?

You are mixing two things together. First of all, Flirc is always acting as a keyboard. It doesn't matter what controller you use in the Flirc GUI.

You are not limited to using Flirc/* nor MCE profiles in the Harmony Hub. Flirc/* profiles are there for the quick start with using Flirc (these profiles are natively supported by Flirc's firmware and are tailored for specific application). You can use almost any other device profile in Harmony and then use Flirc GUI to teach Flirc what must it do when it receive the signal from the remote or blaster.

The MCE keyboard has a complicated protocol which is not supported by Flirc, so you can't use it. What you can do is to add to Harmony some device profile, for example a TV profile (TV profiles usually have biggest number of keys available) for LG, Samsung or Panasonic TV (choose the one you don't have physically in your home) and then use Flirc GUI to assign keyboard combinations you need, for example CTRL+F6 you've mentioned, to remote buttons you want.

I don't know anything on the Echo to Harmony connection and setup so I can't suggest anything on that part.