I did as you suggested and made really certain that the files I was installing were, in fact, going to the correct locations.

My remote started working and I rejoiced. And it worked for a little while and through several reboots just to see if it would still keep working.

And it did until I had accessed the web interface and recorded a few shows. Transcoding was used.

Now I can't even get irw to run without lirc returning to /var/log/lirc:
Jul 10 19:36:12 mythtv lircd 0.7.1: lircd(hauppauge) ready
Jul 10 19:36:40 mythtv lircd 0.7.1: accepted new client on /dev/lircd
Jul 10 19:36:40 mythtv lircd 0.7.1: could not open /dev/lirc
Jul 10 19:36:40 mythtv lircd 0.7.1: default_init(): No such device
Jul 10 19:36:40 mythtv lircd 0.7.1: caught signal

Looks like some investigating on my part to find out why that is happening. I'm doing a cold boot as this is suggesting to see if that clears this up.

Yup. That fixed the error. Now for the million dollar questions:
Why is a cold boot necessary to get my remote back?
Is there a better way?
What caused it to break like that?