Well the IAT sensor had a bad wire on it, which Greg at AntiVenom fixed. That fixed the air temperature errors. This was also plainly visible when I monitored the IAT sensor with HPTuners as random spikes in the temperature value the sensor was reporting.
As for the Random misfires, that is still happening. I have been using HPTuners to monitor the misfires, and it appears to be something vibration sensitive, because it only happens when I am riding down our bumpy dirt road. Hits all cylinders and is not just one or two causing the problem.
I asked Greg to look for the problem this past weekend, and he did find a really boogered up ground that he thought was causing the problem. Unfortunately when I got close to home, I put the monitor on, and found out that the problem is still there.
So at this point, I still don't know what the problem is.
Here's a screen capture showing those misfires: