Great point about the misfire code, I wasn't aware of this. The random misfire is very random when the CEL comes on, and the log sees that it's all the cylinders that are misfiring, so I don't believe it to be a spark issue.
Also, I'm very receptive to learning what is left to do with this tune. So far, I figure the Main VE table needs to be adjusted. I don't know what else to look at.