Today I finished replacing the valve cover gaskets, oil separator, and oil separator hoses. Unfortunately, the Service Engine Soon light is still on, and it is misfiring very bad at low RPMs. Once the RPMs are above 3k, it seems like the misfiring disappears. The SES codes are the following:

P1161
P1347
P1349
P1341

I do not understand why it is misfiring. Could it be the Camshaft Position Sensor? Any other ideas?