One option is to buy an ir learner that comes with a software package.

Companies like Global Cache, Kramer, Command Fusion, and RTI all make these.

There not super cheap, but are great little pieces to own.

You basically plug the learner into the USB input on your computer and load the software. Then you point the remote at the learner and learn each of the commands from the factory remote. After the commands are learned you can convert them into something called hex. The hex commands can then be copied and pasted into most universal remote or home automation programming software packages (not named Harmony).

Or you could just get a new receiver with more common commands.