So I figure it would be neat to remove their software in its entirety and create something new. However, I have no idea where to start. Anyone have any ideas?
So you're talking about writing the main application from scratch? I would think that would be quite a mammoth task if just to get all the remote codes. That's part of the good thing with Logitech - you just tell it your components and it does a sort of generic set up with all the codes retrieved from the central database. Of course if they go bust the remote is basically useless.
It still requires a ton of customisation work though as everyone who has one knows.
One thing that particularly annoys me about the official software is moving the soft buttons around - you have to click, move the mouse to the new location, click, move the mouse to the new location etc...
edit: Or perhaps you're talking about replacing the software on the actual remote control? I think that might be quite a bit harder again.