I have been playing around with the way Pluto handles Lirc in terms of navigation with MythTV.
I have a hack that is working, but obviously it is likely to not be the correct fix, but it does work.
I have install a lircrc file in the /root/.mythtv directory, but I have committed out the parts of the files that Pluto also sends.
0-1, Exit, etc. ( I am not infront of the pluto machine to confirm exactly how I have the file set up, but I will post it later)
The only problem that I have noticed is that if you hit select or enter while you are in the orbital screen it also start MythTV which is running in the background. The fix is to enter MythTV and the exit with the Power button.
I know this is a low level hack, but it does allow greater control than previously. I am still testing, but it does not appear to break another modules.
Also, I have just start working with mythtv, so I have not lost any settings do to upgrade yet, but I did find the fix for the can not connect to backend from this link.