Okay, now I am getting somewhere...
Running as sudo alone did not do the trick, but adding the udev rule got me most of the way up and running. When running the GUI, I still periodically get disconnects that drop and then reconnect right away. If I try to record a key, it tells me there is no more space.
Running the CLI, keys tells me that the list is empty, though most keys automatically register when pressed in the GUI (I am running a Harmony using the Flirc profile). If I run space, it will randomly insert "usb transfer failed, error code[-1] Input/Output error" but still give me the keys information (165 keys, 3 remaining, using 5500% memory?). I also tried to record to see if it was picking up ghost signals, but it gives me an error that there is no space left on the device. Initially in my front USB port it would then type an endless string of the character I was recording, without me pushing a button. I switched the Flirc to the rear USB port and now I do not get the string, just the no space left on device error. It seems that switching the port also got rid of the usb transfer failed errors when running space. Hopefully most of that was just some ghost signals it was picking up.
Thanks for your great support on this site, I am usually able to fix my issues by searching through the forums but this time I felt I needed to reach out because I am a bit stumped.