I got this working, and it was helluva lot simpler than I had been going after. There were a few key settings that made everything just fall into place and "just work".
First and foremost find out what works best for YOUR STB. From everything I've read Motorola's like Broadcast @ 400mbps. Most articles I've read tell you use Point to Point (P2P), this failed every single time for me. So Broadcast and 400mbps (this is in back end settings for your device).
That is really all I needed to do to get it working, but here are my notes on if it does fail how you can prime the STB.
First we need to grab some files to build "firewire_tester"
sudo apt-get install libiec61883-dev build-essential libraw1394-dev libiec61883-dev libavc1394-dev wget
Next we want to change to /usr/local/bin then grab firewire_tester.c
cd /usr/local/bin sudo wget "http://cvs.mythtv.org/trac/browser/trunk/mythtv/contrib/development/firewire_tester/firewire_tester.c?format=txt" -O firewire_tester.c
Let's compile firewire_tester.c
gcc -Wall -o firewire_tester firewire_tester.c -liec61883 -lraw1394
Now we have to make firewire_primer.pl executable
sudo chmod +x /usr/share/doc/mythtv-backend/contrib/user_jobs/firewire_primer.pl
Create a link to firewire_primer.pl (should still be in /usr/local/bin)
sudo ln -s /usr/share/doc/mythtv-backend/contrib/user_jobs/firewire_primer.pl firewire_primer.pl
Test your connection (should not have TV on while doing this)