Well, I went ahead and ordered this ugly monstrosity. It's coming from Singapore, so it'll be a few weeks before it get here.
Harmony Ultimate is here, and it controls everything I have except Fire TV. Aaaaarrrghhh! I'm ready to pull my hair out over here.
Last chance. I'm ordering one of those cheap USB IR receivers that people over at AVS Forums are saying work well with Fire TV, and teaching my Harmony the basic buttons (left, right, up, down, select, back, home.) If that doesn't work - all of it is going back to their respective manufacturers until they learn how to play nice with each other.
Victory! After hooking up the IR receiver from the MCE remote to Fire TV, and teaching Harmony the basic keys, I can now control everything in my setup with a single remote. Of course the voice input from the Fire TV remote is missing, and since Harmony Ultimate has no keyboard, I'm stuck doing text entry letter-by-letter via the clunky mid-90's interface. It'll do for now, until I figure out a way to either bring QWERTY to Harmony, or get a USB hub for Fire TV so that I can use my RF micro-keyboard.
Now I need to do some wire management to take care of the spaghetti wiring from all these devices.
Got a simple unpowered 4-port USB hub, plugged in both the IR receiver and an RF receiver, so now I can also use a micro-keyboard for doing text input. The living room is now wife-approved!