If your system is finished except for this portion, you're either going to be lucky or you'll have a heck of a challenge. Installing an IR extending system requires running wires from place to place -- are these "places" covered up and finished off?

I'm surprised at "Only a basic Harmony remote,... if they are still available, will control your equipment directly by IR." If the intention here was to say "you can control your equipment directly by IR with as little as just a Harmony remote," then that's true. But there are other brands of remote control systems that have IR-only solutions. As mentioned, though, the programming of these requires training, and that's only available to dealers.

I'd say it's time to find a pro to finish off your system.