So my story from the original post didn't change much. Same things happened on and off. At one point I got a message that told me I couldn't exceed 15 mph. At the time, I was travelling between Houston and Lake Texoma for Memorial Day weekend (had dogs in the truck with us). Truck didn't feel any different. I slowed down, sped up, everything felt/sounded/smelled/looked normal. Luckily, we weren't far from a dealership. Pulled over there to have it checked out. Was told again that it was nothing to worry about, but there were some updates that could be done to the system. we left there and the CEL cleared at some point on the trip.
I did the updates sometime after the trip. The updates stopped the message about filter regeneration, but didn't stop the CEL.
A year later, I racked up all of the recalls on the truck (about 7 or 8 of them), plus the CEL issue, but the final straw was my door locks stopped working. See thread here
. Turns out it was my catalytic converter causing the CEL. None of the other dealers said that, they always just said it was the DEF system. Haven't had any issues on the CEL since.
So if you're experiencing CEL, filter regeneration problems, drive at a maximum of 15 mph problems, it could be your catalytic converter. Same thing happened to a co-worker of mine. He said he even got a blue screen of death; I don't recall ever getting that.
Just wanted to bring this thread full circle in case anyone else is experiencing similar problems.