p0300 and p0316 all of the sudden

Well, in true Mustang fashion, now that I have gotten past my latest problem, I have immediately gained a new one.:banghead: I recently had my my tuner send a tune for my emissions. I'm pretty sure it was my normal tune with all the sensors turned on. After throwing some emissions related tunes then having to replace an o2, the car cleared everything out and I passed my inspection yesterday. Today it threw codes p0300 and p0316 for random misfire. I have not returned to the normal tune because in about a week I was going to maybe try someone different for tuning since my current guy is sorta flakey. I'm pretty sure I have not noticed the car running different at all and have not noticed any misfiring. Anyone know what may cause this and how to fix it. Thanks